From 6059ead55bdd7b26a7ba0fefa32b33df3d3be793 Mon Sep 17 00:00:00 2001 From: Katarzyna Sikora Date: Tue, 20 Aug 2024 10:03:28 +0200 Subject: [PATCH 01/35] Dev ks (#1042) * rm cp from snpsplit * genome_alias Snakefile --------- Co-authored-by: katarzyna.otylia.sikora@gmail.com --- snakePipes/shared/rules/masked_genomeIndex.snakefile | 9 ++++----- snakePipes/workflows/DNAmapping/Snakefile | 5 +++-- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/snakePipes/shared/rules/masked_genomeIndex.snakefile b/snakePipes/shared/rules/masked_genomeIndex.snakefile index 6eaddb72e..028bc5e83 100644 --- a/snakePipes/shared/rules/masked_genomeIndex.snakefile +++ b/snakePipes/shared/rules/masked_genomeIndex.snakefile @@ -2,7 +2,8 @@ from os.path import join, dirname import glob GENOMEDIR = os.path.dirname(genome_fasta) -BASENAME = genome +genome_alias = os.path.splitext(os.path.basename(genome))[0] +BASENAME = genome_alias # define snpgenome_dir if allele_hybrid == 'dual': SNPdir = "snp_genome/" + strains[0] + "_" + \ @@ -50,8 +51,7 @@ else: params: strain1 = strains[0], SNPpath = os.path.abspath(VCFfile), - - temp_out=temp("all_SNPs_" + strains[0] + "_GRCm38.txt.gz"), + temp_out=temp("all_SNPs_" + strains[0] + "_" + genome_alias + ".txt.gz"), out_bname=os.path.basename(SNPFile) conda: CONDA_SHARED_ENV shell: @@ -59,8 +59,7 @@ else: " SNPsplit_genome_preparation" " --genome_build {BASENAME}" " --reference_genome {input.genome} --vcf_file {params.SNPpath}" - " --strain {params.strain1} && cp " - "{params.temp_out} {params.out_bname}" + " --strain {params.strain1}" "&& cd ../" if aligner == "STAR": diff --git a/snakePipes/workflows/DNAmapping/Snakefile b/snakePipes/workflows/DNAmapping/Snakefile index f5f2c2c9e..579d10430 100755 --- a/snakePipes/workflows/DNAmapping/Snakefile +++ b/snakePipes/workflows/DNAmapping/Snakefile @@ -54,15 +54,16 @@ include: os.path.join(maindir, "shared", "rules", "multiQC.snakefile") ## Allele-specific JOBs if "allelic-mapping" in mode: + genome_alias = os.path.splitext(os.path.basename(genome))[0] # Updated global vars if mode = "allelic-mapping" if allele_mode == 'create_and_map': bowtie2_index_allelic = 'snp_genome/bowtie2_Nmasked/Genome.1.bt2' if len(strains) == 1: allele_hybrid = 'single' - SNPFile = "snp_genome/all_SNPs_" + strains[0] + "_" + genome + ".txt.gz" + SNPFile = "snp_genome/all_SNPs_" + strains[0] + "_" + genome_alias + ".txt.gz" elif len(strains) == 2: allele_hybrid = 'dual' - SNPFile = "snp_genome/all_" + strains[1] + "_SNPs_" + strains[0] + "_reference.based_on_" + genome + ".txt" + SNPFile = SNPFile = "snp_genome/all_" + strains[1] + "_SNPs_" + strains[0] + "_reference.based_on_" + genome_alias + ".txt" include: os.path.join(maindir, "shared", "rules", "masked_genomeIndex.snakefile") elif allele_mode == 'map_only': From 6b1e9f9775dd10302d61ea2ba6582a386547e3d3 Mon Sep 17 00:00:00 2001 From: Katarzyna Sikora Date: Tue, 20 Aug 2024 12:17:04 +0200 Subject: [PATCH 02/35] Dev ks (#1043) * bump multiqc version --------- Co-authored-by: katarzyna.otylia.sikora@gmail.com --- snakePipes/shared/rules/envs/shared.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/snakePipes/shared/rules/envs/shared.yaml b/snakePipes/shared/rules/envs/shared.yaml index 79e5e2e46..fcf45b73e 100755 --- a/snakePipes/shared/rules/envs/shared.yaml +++ b/snakePipes/shared/rules/envs/shared.yaml @@ -12,7 +12,7 @@ dependencies: - fastqc = 0.12.1 - cutadapt = 4.6 - trim-galore = 0.6.10 - - multiqc = 1.19 + - multiqc = 1.23 - fastp = 0.23.4 - umi_tools = 1.1.4 - fq = 0.11.0 From 576230cbe5d5aad425a7cb461723c1d00de37ffe Mon Sep 17 00:00:00 2001 From: "katarzyna.otylia.sikora@gmail.com" Date: Thu, 5 Sep 2024 12:23:32 +0200 Subject: [PATCH 03/35] sed test dag --- .ci_stuff/test_dag.sh | 234 +++++++++++++++++++++--------------------- 1 file changed, 117 insertions(+), 117 deletions(-) diff --git a/.ci_stuff/test_dag.sh b/.ci_stuff/test_dag.sh index 255ffddbe..51062b612 100755 --- a/.ci_stuff/test_dag.sh +++ b/.ci_stuff/test_dag.sh @@ -160,282 +160,282 @@ touch /tmp/genes.t2g snakePipes config --tempDir /tmp # createIndices -WC=`createIndices -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --genome ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.gz --gtf ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz blah | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`createIndices -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --genome ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.gz --gtf ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz blah | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 210 ]; then exit 1 ; fi -WC=`createIndices -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --genome ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.gz --gtf ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz --rmskURL http://hgdownload.soe.ucsc.edu/goldenPath/dm6/database/rmsk.txt.gz blah | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`createIndices -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --genome ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.gz --gtf ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz --rmskURL http://hgdownload.soe.ucsc.edu/goldenPath/dm6/database/rmsk.txt.gz blah | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 218 ]; then exit 1 ; fi -WC=`createIndices -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --genome ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.gz --gtf ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz --rmskURL http://hgdownload.soe.ucsc.edu/goldenPath/dm6/database/rmsk.txt.gz blah | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`createIndices -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --genome ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.gz --gtf ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz --rmskURL http://hgdownload.soe.ucsc.edu/goldenPath/dm6/database/rmsk.txt.gz blah | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 218 ]; then exit 1 ; fi # spikein -WC=`createIndices -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --genomeURL ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.gz --gtfURL ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz --spikeinGenomeURL ftp://ftp.ensembl.org/pub/release-79/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.dna_sm.toplevel.fa.gz --spikeinGtfURL ftp://ftp.ensembl.org/pub/release-96/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.22.96.gtf.gz --rmskURL http://hgdownload.soe.ucsc.edu/goldenPath/dm6/database/rmsk.txt.gz blah | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`createIndices -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --genomeURL ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.gz --gtfURL ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz --spikeinGenomeURL ftp://ftp.ensembl.org/pub/release-79/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.dna_sm.toplevel.fa.gz --spikeinGtfURL ftp://ftp.ensembl.org/pub/release-96/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.22.96.gtf.gz --rmskURL http://hgdownload.soe.ucsc.edu/goldenPath/dm6/database/rmsk.txt.gz blah | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 261 ]; then exit 1 ; fi # DNA mapping -WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp " | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp " | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1305 ]; then exit 1 ; fi -WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --dedup --properPairs | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --dedup --properPairs | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1397 ]; then exit 1 ; fi -WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --dedup --properPairs --bcExtract | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --dedup --properPairs --bcExtract | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1323 ]; then exit 1 ; fi -WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --UMIDedup --properPairs --bcExtract | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --UMIDedup --properPairs --bcExtract | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1397 ]; then exit 1 ; fi -WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --UMIDedup --properPairs | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --UMIDedup --properPairs | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1471 ]; then exit 1 ; fi -WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --trim --mapq 20 --UMIDedup --properPairs | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --trim --mapq 20 --UMIDedup --properPairs | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1471 ]; then exit 1 ; fi -WC=`DNAmapping -i SE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`DNAmapping -i SE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1157 ]; then exit 1 ; fi -WC=`DNAmapping -i SE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --dedup --properPairs | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`DNAmapping -i SE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --dedup --properPairs | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1249 ]; then exit 1 ; fi -WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --trim --aligner bwa | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --trim --aligner bwa | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1296 ]; then exit 1 ; fi -WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --trim --aligner bwa-mem2 | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --trim --aligner bwa-mem2 | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1296 ]; then exit 1 ; fi #allelic -WC=`DNAmapping -m allelic-mapping -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`DNAmapping -m allelic-mapping -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2237 ]; then exit 1 ; fi -WC=`DNAmapping -m allelic-mapping -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`DNAmapping -m allelic-mapping -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2218 ]; then exit 1 ; fi -WC=`DNAmapping -m allelic-mapping -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`DNAmapping -m allelic-mapping -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2237 ]; then exit 1 ; fi # ChIPseq -WC=`ChIPseq -d BAM_input --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d BAM_input --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 368 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d BAM_input --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 347 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 568 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_broad_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_broad_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 736 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 537 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --singleEnd .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --singleEnd .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 566 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --bigWigType log2ratio .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --bigWigType log2ratio .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 506 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller SEACR .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller SEACR .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 823 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller SEACR --useSpikeInForNorm .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller SEACR --useSpikeInForNorm .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1235 ]; then exit 1 ; fi #noInput -WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 365 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 307 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller SEACR .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller SEACR .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 569 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller SEACR --useSpikeInForNorm .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller SEACR --useSpikeInForNorm .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 781 ]; then exit 1 ; fi # fromBAM -WC=`ChIPseq -d outdir --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d outdir --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1092 ]; then exit 1 ; fi # fromBam and noInput -WC=`ChIPseq -d outdir --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d outdir --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 739 ]; then exit 1 ; fi # spikein -WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1033 ]; then exit 1 ; fi # spikein and noInput -WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 633 ]; then exit 1 ; fi # fromBAM and spikein -WC=`ChIPseq -d outdir --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d outdir --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1329 ]; then exit 1 ; fi -WC=`ChIPseq -d outdir --useSpikeInForNorm --getSizeFactorsFrom TSS --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d outdir --useSpikeInForNorm --getSizeFactorsFrom TSS --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1086 ]; then exit 1 ; fi -WC=`ChIPseq -d outdir --useSpikeInForNorm --getSizeFactorsFrom input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d outdir --useSpikeInForNorm --getSizeFactorsFrom input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1058 ]; then exit 1 ; fi # allelic -WC=`ChIPseq -d allelic_BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_short_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d allelic_BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_short_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 385 ]; then exit 1 ; fi #multiComp -WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 757 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 760 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_broad_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_broad_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 925 ]; then exit 1 ; fi #multiComp and fromBam -WC=`ChIPseq -d outdir --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d outdir --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1281 ]; then exit 1 ; fi -WC=`ChIPseq -d outdir --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d outdir --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1284 ]; then exit 1 ; fi #multiComp and spikein -WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1205 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1208 ]; then exit 1 ; fi #multiComp and spikein and noInput -WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 771 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 747 ]; then exit 1 ; fi #multiComp and spikein and fromBam -WC=`ChIPseq -d outdir --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d outdir --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1501 ]; then exit 1 ; fi -WC=`ChIPseq -d outdir --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d outdir --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 947 ]; then exit 1 ; fi #multiComp and spikein and fromBam and noInput -WC=`ChIPseq -d outdir --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d outdir --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 971 ]; then exit 1 ; fi -WC=`ChIPseq -d outdir --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d outdir --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 947 ]; then exit 1 ; fi #multiComp and noInput and fromBam -WC=`ChIPseq -d outdir --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller SEACR --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ChIPseq -d outdir --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller SEACR --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1081 ]; then exit 1 ; fi # mRNAseq -WC=`mRNAseq -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`mRNAseq -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1536 ]; then exit 1 ; fi -WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1547 ]; then exit 1 ; fi -WC=`mRNAseq -i PE_input -o output --rMats --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`mRNAseq -i PE_input -o output --rMats --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1566 ]; then exit 1 ; fi -WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1106 ]; then exit 1 ; fi -WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1639 ]; then exit 1 ; fi -WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment-free,deepTools_qc" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment-free,deepTools_qc" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1736 ]; then exit 1 ; fi -WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --bcExtract --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --bcExtract --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1565 ]; then exit 1 ; fi -WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --bcExtract --UMIDedup --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --bcExtract --UMIDedup --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1639 ]; then exit 1 ; fi -WC=`mRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`mRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1389 ]; then exit 1 ; fi -WC=`mRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`mRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 958 ]; then exit 1 ; fi -WC=`mRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`mRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1481 ]; then exit 1 ; fi -WC=`mRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment-free,deepTools_qc" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`mRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment-free,deepTools_qc" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1578 ]; then exit 1 ; fi -WC=`mRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --fastqc .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`mRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --fastqc .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1665 ]; then exit 1 ; fi -WC=`mRNAseq -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`mRNAseq -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1058 ]; then exit 1 ; fi #multiple comparison groups -WC=`mRNAseq --mode alignment,alignment-free -i PE_input -o output --rMats --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`mRNAseq --mode alignment,alignment-free -i PE_input -o output --rMats --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1476 ]; then exit 1 ; fi # three prime sequencing -WC=`mRNAseq -i PE_input -o output --mode three-prime-seq --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`mRNAseq -i PE_input -o output --mode three-prime-seq --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1668 ]; then exit 1 ; fi -WC=`mRNAseq -i PE_input -o output --mode three-prime-seq,deepTools_qc --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`mRNAseq -i PE_input -o output --mode three-prime-seq,deepTools_qc --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2109 ]; then exit 1 ; fi #allelic -WC=`mRNAseq -m allelic-mapping,deepTools_qc -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`mRNAseq -m allelic-mapping,deepTools_qc -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2304 ]; then exit 1 ; fi -WC=`mRNAseq -m allelic-mapping,deepTools_qc -i allelic_BAM_input/filtered_bam --fromBAM --bamExt '.filtered.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`mRNAseq -m allelic-mapping,deepTools_qc -i allelic_BAM_input/filtered_bam --fromBAM --bamExt '.filtered.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1285 ]; then exit 1 ; fi -WC=`mRNAseq -m allelic-mapping,deepTools_qc -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`mRNAseq -m allelic-mapping,deepTools_qc -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2315 ]; then exit 1 ; fi -WC=`mRNAseq -m allelic-mapping,deepTools_qc -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`mRNAseq -m allelic-mapping,deepTools_qc -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2296 ]; then exit 1 ; fi -WC=`mRNAseq -m allelic-mapping,deepTools_qc -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`mRNAseq -m allelic-mapping,deepTools_qc -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2315 ]; then exit 1 ; fi -WC=`mRNAseq -m allelic-mapping,deepTools_qc,alignment-free -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`mRNAseq -m allelic-mapping,deepTools_qc,alignment-free -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 3012 ]; then exit 1 ; fi -WC=`mRNAseq -m allelic-counting -i allelic_BAM_input/allelic_bams --fromBAM --bamExt '.sorted.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`mRNAseq -m allelic-counting -i allelic_BAM_input/allelic_bams --fromBAM --bamExt '.sorted.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 638 ]; then exit 1 ; fi -WC=`mRNAseq -m allelic-counting -i allelic_BAM_input/allelic_bams --fromBAM --bamExt '.sorted.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`mRNAseq -m allelic-counting -i allelic_BAM_input/allelic_bams --fromBAM --bamExt '.sorted.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 638 ]; then exit 1 ; fi #allelic+multicomp -WC=`mRNAseq -m allelic-counting -i allelic_BAM_input/allelic_bams --fromBAM --bamExt '.sorted.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`mRNAseq -m allelic-counting -i allelic_BAM_input/allelic_bams --fromBAM --bamExt '.sorted.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 668 ]; then exit 1 ; fi -WC=`mRNAseq -m allelic-mapping,deepTools_qc -i allelic_BAM_input/filtered_bam --fromBAM --bamExt '.filtered.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`mRNAseq -m allelic-mapping,deepTools_qc -i allelic_BAM_input/filtered_bam --fromBAM --bamExt '.filtered.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1315 ]; then exit 1 ; fi -WC=`mRNAseq -m allelic-mapping,deepTools_qc,alignment-free -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`mRNAseq -m allelic-mapping,deepTools_qc,alignment-free -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 3021 ]; then exit 1 ; fi #ncRNAseq -WC=`ncRNAseq -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ncRNAseq -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1269 ]; then exit 1 ; fi -WC=`ncRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ncRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1289 ]; then exit 1 ; fi -WC=`ncRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ncRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1131 ]; then exit 1 ; fi -WC=`ncRNAseq -i BAM_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ncRNAseq -i BAM_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 901 ]; then exit 1 ; fi #multiple comparison groups -WC=`ncRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ncRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1317 ]; then exit 1 ; fi # scRNAseq -#WC=`scRNAseq -i PE_input -o output --mode Gruen --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +#WC=`scRNAseq -i PE_input -o output --mode Gruen --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` #if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1038 ]; then exit 1 ; fi -#WC=`scRNAseq -i PE_input -o output --mode Gruen --snakemakeOptions " --dryrun --conda-prefix /tmp" --skipRaceID --splitLib .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +#WC=`scRNAseq -i PE_input -o output --mode Gruen --snakemakeOptions " --dryrun --conda-prefix /tmp" --skipRaceID --splitLib .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` #if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1015 ]; then exit 1 ; fi -WC=`scRNAseq -i PE_input -o output --mode STARsolo --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`scRNAseq -i PE_input -o output --mode STARsolo --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1642 ]; then exit 1 ; fi -WC=`scRNAseq -i PE_input -o output --mode STARsolo --skipVelocyto --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`scRNAseq -i PE_input -o output --mode STARsolo --skipVelocyto --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1467 ]; then exit 1 ; fi -WC=`scRNAseq -i PE_input -o output --mode Alevin --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`scRNAseq -i PE_input -o output --mode Alevin --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 714 ]; then exit 1 ; fi -WC=`scRNAseq -i PE_input -o output --mode Alevin --skipVelocyto --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`scRNAseq -i PE_input -o output --mode Alevin --skipVelocyto --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 604 ]; then exit 1 ; fi # WGBS -WC=`WGBS -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`WGBS -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1300 ]; then exit 1 ; fi -WC=`WGBS -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`WGBS -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1343 ]; then exit 1 ; fi -WC=`WGBS -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --aligner bwameth2 --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`WGBS -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --aligner bwameth2 --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1343 ]; then exit 1 ; fi -WC=`WGBS -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --GCbias .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`WGBS -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --GCbias .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1353 ]; then exit 1 ; fi -WC=`WGBS -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --fromBAM --snakemakeOptions " --dryrun --conda-prefix /tmp" --GCbias .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`WGBS -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --fromBAM --snakemakeOptions " --dryrun --conda-prefix /tmp" --GCbias .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 974 ]; then exit 1 ; fi -WC=`WGBS -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --fromBAM --fastqc --snakemakeOptions " --dryrun --conda-prefix /tmp" --GCbias .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`WGBS -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --fromBAM --fastqc --snakemakeOptions " --dryrun --conda-prefix /tmp" --GCbias .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 974 ]; then exit 1 ; fi -WC=`WGBS -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --fromBAM --skipBamQC --snakemakeOptions " --dryrun --conda-prefix /tmp" --GCbias .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`WGBS -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --fromBAM --skipBamQC --snakemakeOptions " --dryrun --conda-prefix /tmp" --GCbias .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 530 ]; then exit 1 ; fi # ATACseq -WC=`ATACseq -d BAM_input --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ATACseq -d BAM_input --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 460 ]; then exit 1 ; fi -WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 605 ]; then exit 1 ; fi -WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 706 ]; then exit 1 ; fi -WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller HMMRATAC .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller HMMRATAC .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 697 ]; then exit 1 ; fi -WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --maxFragmentSize 120 --qval 0.1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --maxFragmentSize 120 --qval 0.1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 605 ]; then exit 1 ; fi -WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1055 ]; then exit 1 ; fi #multicomp -WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 743 ]; then exit 1 ; fi -WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 860 ]; then exit 1 ; fi -WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller HMMRATAC .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller HMMRATAC .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 835 ]; then exit 1 ; fi -WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --maxFragmentSize 120 --qval 0.1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --maxFragmentSize 120 --qval 0.1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 743 ]; then exit 1 ; fi -WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1193 ]; then exit 1 ; fi # HiC -WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --correctionMethod ICE .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --correctionMethod ICE .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 965 ]; then exit 1 ; fi -WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 891 ]; then exit 1 ; fi -WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 983 ]; then exit 1 ; fi -WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --enzyme DpnII .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --enzyme DpnII .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 891 ]; then exit 1 ; fi -WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --noTAD .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --noTAD .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 808 ]; then exit 1 ; fi -WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --aligner bwa-mem2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --aligner bwa-mem2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 891 ]; then exit 1 ; fi # preprocessing -WC=`preprocessing -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --fastqc --optDedupDist 2500 | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`preprocessing -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --fastqc --optDedupDist 2500 | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 761 ]; then exit 1 ; fi -WC=`preprocessing -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --fastqc --optDedupDist 2500 | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | wc -l` +WC=`preprocessing -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --fastqc --optDedupDist 2500 | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 761 ]; then exit 1 ; fi rm -rf SE_input PE_input BAM_input output allelic_input allelic_BAM_input /tmp/genes.gtf /tmp/genome.fa /tmp/genome.fa.fai /tmp/rmsk.txt /tmp/genes.bed /tmp/spikein_genes.gtf From 8bcdfb8b53ed792f2f5d7774dfafb582dbfadf3b Mon Sep 17 00:00:00 2001 From: "katarzyna.otylia.sikora@gmail.com" Date: Thu, 5 Sep 2024 13:10:37 +0200 Subject: [PATCH 04/35] sed test dag --- .ci_stuff/test_dag.sh | 234 +++++++++++++++++++++--------------------- 1 file changed, 117 insertions(+), 117 deletions(-) diff --git a/.ci_stuff/test_dag.sh b/.ci_stuff/test_dag.sh index 51062b612..d336a8fc3 100755 --- a/.ci_stuff/test_dag.sh +++ b/.ci_stuff/test_dag.sh @@ -160,282 +160,282 @@ touch /tmp/genes.t2g snakePipes config --tempDir /tmp # createIndices -WC=`createIndices -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --genome ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.gz --gtf ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz blah | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`createIndices -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --genome ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.gz --gtf ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz blah | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 210 ]; then exit 1 ; fi -WC=`createIndices -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --genome ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.gz --gtf ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz --rmskURL http://hgdownload.soe.ucsc.edu/goldenPath/dm6/database/rmsk.txt.gz blah | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`createIndices -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --genome ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.gz --gtf ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz --rmskURL http://hgdownload.soe.ucsc.edu/goldenPath/dm6/database/rmsk.txt.gz blah | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 218 ]; then exit 1 ; fi -WC=`createIndices -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --genome ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.gz --gtf ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz --rmskURL http://hgdownload.soe.ucsc.edu/goldenPath/dm6/database/rmsk.txt.gz blah | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`createIndices -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --genome ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.gz --gtf ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz --rmskURL http://hgdownload.soe.ucsc.edu/goldenPath/dm6/database/rmsk.txt.gz blah | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 218 ]; then exit 1 ; fi # spikein -WC=`createIndices -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --genomeURL ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.gz --gtfURL ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz --spikeinGenomeURL ftp://ftp.ensembl.org/pub/release-79/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.dna_sm.toplevel.fa.gz --spikeinGtfURL ftp://ftp.ensembl.org/pub/release-96/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.22.96.gtf.gz --rmskURL http://hgdownload.soe.ucsc.edu/goldenPath/dm6/database/rmsk.txt.gz blah | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`createIndices -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --genomeURL ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.gz --gtfURL ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz --spikeinGenomeURL ftp://ftp.ensembl.org/pub/release-79/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.dna_sm.toplevel.fa.gz --spikeinGtfURL ftp://ftp.ensembl.org/pub/release-96/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.22.96.gtf.gz --rmskURL http://hgdownload.soe.ucsc.edu/goldenPath/dm6/database/rmsk.txt.gz blah | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 261 ]; then exit 1 ; fi # DNA mapping -WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp " | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp " | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1305 ]; then exit 1 ; fi -WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --dedup --properPairs | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --dedup --properPairs | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1397 ]; then exit 1 ; fi -WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --dedup --properPairs --bcExtract | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --dedup --properPairs --bcExtract | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1323 ]; then exit 1 ; fi -WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --UMIDedup --properPairs --bcExtract | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --UMIDedup --properPairs --bcExtract | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1397 ]; then exit 1 ; fi -WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --UMIDedup --properPairs | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --UMIDedup --properPairs | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1471 ]; then exit 1 ; fi -WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --trim --mapq 20 --UMIDedup --properPairs | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --trim --mapq 20 --UMIDedup --properPairs | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1471 ]; then exit 1 ; fi -WC=`DNAmapping -i SE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`DNAmapping -i SE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1157 ]; then exit 1 ; fi -WC=`DNAmapping -i SE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --dedup --properPairs | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`DNAmapping -i SE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --dedup --properPairs | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1249 ]; then exit 1 ; fi -WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --trim --aligner bwa | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --trim --aligner bwa | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1296 ]; then exit 1 ; fi -WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --trim --aligner bwa-mem2 | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --trim --aligner bwa-mem2 | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1296 ]; then exit 1 ; fi #allelic -WC=`DNAmapping -m allelic-mapping -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`DNAmapping -m allelic-mapping -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2237 ]; then exit 1 ; fi -WC=`DNAmapping -m allelic-mapping -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`DNAmapping -m allelic-mapping -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2218 ]; then exit 1 ; fi -WC=`DNAmapping -m allelic-mapping -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`DNAmapping -m allelic-mapping -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2237 ]; then exit 1 ; fi # ChIPseq -WC=`ChIPseq -d BAM_input --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d BAM_input --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 368 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d BAM_input --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 347 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 568 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_broad_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_broad_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 736 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 537 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --singleEnd .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --singleEnd .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 566 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --bigWigType log2ratio .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --bigWigType log2ratio .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 506 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller SEACR .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller SEACR .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 823 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller SEACR --useSpikeInForNorm .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller SEACR --useSpikeInForNorm .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1235 ]; then exit 1 ; fi #noInput -WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 365 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 307 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller SEACR .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller SEACR .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 569 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller SEACR --useSpikeInForNorm .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller SEACR --useSpikeInForNorm .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 781 ]; then exit 1 ; fi # fromBAM -WC=`ChIPseq -d outdir --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d outdir --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1092 ]; then exit 1 ; fi # fromBam and noInput -WC=`ChIPseq -d outdir --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d outdir --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 739 ]; then exit 1 ; fi # spikein -WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1033 ]; then exit 1 ; fi # spikein and noInput -WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 633 ]; then exit 1 ; fi # fromBAM and spikein -WC=`ChIPseq -d outdir --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d outdir --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1329 ]; then exit 1 ; fi -WC=`ChIPseq -d outdir --useSpikeInForNorm --getSizeFactorsFrom TSS --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d outdir --useSpikeInForNorm --getSizeFactorsFrom TSS --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1086 ]; then exit 1 ; fi -WC=`ChIPseq -d outdir --useSpikeInForNorm --getSizeFactorsFrom input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d outdir --useSpikeInForNorm --getSizeFactorsFrom input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1058 ]; then exit 1 ; fi # allelic -WC=`ChIPseq -d allelic_BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_short_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d allelic_BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_short_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 385 ]; then exit 1 ; fi #multiComp -WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 757 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 760 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_broad_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_broad_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 925 ]; then exit 1 ; fi #multiComp and fromBam -WC=`ChIPseq -d outdir --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d outdir --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1281 ]; then exit 1 ; fi -WC=`ChIPseq -d outdir --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d outdir --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1284 ]; then exit 1 ; fi #multiComp and spikein -WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1205 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1208 ]; then exit 1 ; fi #multiComp and spikein and noInput -WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 771 ]; then exit 1 ; fi -WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 747 ]; then exit 1 ; fi #multiComp and spikein and fromBam -WC=`ChIPseq -d outdir --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d outdir --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1501 ]; then exit 1 ; fi -WC=`ChIPseq -d outdir --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d outdir --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 947 ]; then exit 1 ; fi #multiComp and spikein and fromBam and noInput -WC=`ChIPseq -d outdir --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d outdir --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 971 ]; then exit 1 ; fi -WC=`ChIPseq -d outdir --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d outdir --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 947 ]; then exit 1 ; fi #multiComp and noInput and fromBam -WC=`ChIPseq -d outdir --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller SEACR --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ChIPseq -d outdir --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller SEACR --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_noControl_config.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1081 ]; then exit 1 ; fi # mRNAseq -WC=`mRNAseq -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`mRNAseq -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1536 ]; then exit 1 ; fi -WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1547 ]; then exit 1 ; fi -WC=`mRNAseq -i PE_input -o output --rMats --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`mRNAseq -i PE_input -o output --rMats --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1566 ]; then exit 1 ; fi -WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1106 ]; then exit 1 ; fi -WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1639 ]; then exit 1 ; fi -WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment-free,deepTools_qc" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment-free,deepTools_qc" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1736 ]; then exit 1 ; fi -WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --bcExtract --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --bcExtract --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1565 ]; then exit 1 ; fi -WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --bcExtract --UMIDedup --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`mRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --bcExtract --UMIDedup --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1639 ]; then exit 1 ; fi -WC=`mRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`mRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1389 ]; then exit 1 ; fi -WC=`mRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`mRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 958 ]; then exit 1 ; fi -WC=`mRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`mRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1481 ]; then exit 1 ; fi -WC=`mRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment-free,deepTools_qc" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`mRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment-free,deepTools_qc" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1578 ]; then exit 1 ; fi -WC=`mRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --fastqc .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`mRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --fastqc .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1665 ]; then exit 1 ; fi -WC=`mRNAseq -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`mRNAseq -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1058 ]; then exit 1 ; fi #multiple comparison groups -WC=`mRNAseq --mode alignment,alignment-free -i PE_input -o output --rMats --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`mRNAseq --mode alignment,alignment-free -i PE_input -o output --rMats --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1476 ]; then exit 1 ; fi # three prime sequencing -WC=`mRNAseq -i PE_input -o output --mode three-prime-seq --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`mRNAseq -i PE_input -o output --mode three-prime-seq --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1668 ]; then exit 1 ; fi -WC=`mRNAseq -i PE_input -o output --mode three-prime-seq,deepTools_qc --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`mRNAseq -i PE_input -o output --mode three-prime-seq,deepTools_qc --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2109 ]; then exit 1 ; fi #allelic -WC=`mRNAseq -m allelic-mapping,deepTools_qc -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`mRNAseq -m allelic-mapping,deepTools_qc -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2304 ]; then exit 1 ; fi -WC=`mRNAseq -m allelic-mapping,deepTools_qc -i allelic_BAM_input/filtered_bam --fromBAM --bamExt '.filtered.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`mRNAseq -m allelic-mapping,deepTools_qc -i allelic_BAM_input/filtered_bam --fromBAM --bamExt '.filtered.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1285 ]; then exit 1 ; fi -WC=`mRNAseq -m allelic-mapping,deepTools_qc -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`mRNAseq -m allelic-mapping,deepTools_qc -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2315 ]; then exit 1 ; fi -WC=`mRNAseq -m allelic-mapping,deepTools_qc -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`mRNAseq -m allelic-mapping,deepTools_qc -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2296 ]; then exit 1 ; fi -WC=`mRNAseq -m allelic-mapping,deepTools_qc -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`mRNAseq -m allelic-mapping,deepTools_qc -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2315 ]; then exit 1 ; fi -WC=`mRNAseq -m allelic-mapping,deepTools_qc,alignment-free -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`mRNAseq -m allelic-mapping,deepTools_qc,alignment-free -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 3012 ]; then exit 1 ; fi -WC=`mRNAseq -m allelic-counting -i allelic_BAM_input/allelic_bams --fromBAM --bamExt '.sorted.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`mRNAseq -m allelic-counting -i allelic_BAM_input/allelic_bams --fromBAM --bamExt '.sorted.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 638 ]; then exit 1 ; fi -WC=`mRNAseq -m allelic-counting -i allelic_BAM_input/allelic_bams --fromBAM --bamExt '.sorted.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`mRNAseq -m allelic-counting -i allelic_BAM_input/allelic_bams --fromBAM --bamExt '.sorted.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 638 ]; then exit 1 ; fi #allelic+multicomp -WC=`mRNAseq -m allelic-counting -i allelic_BAM_input/allelic_bams --fromBAM --bamExt '.sorted.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`mRNAseq -m allelic-counting -i allelic_BAM_input/allelic_bams --fromBAM --bamExt '.sorted.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 668 ]; then exit 1 ; fi -WC=`mRNAseq -m allelic-mapping,deepTools_qc -i allelic_BAM_input/filtered_bam --fromBAM --bamExt '.filtered.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`mRNAseq -m allelic-mapping,deepTools_qc -i allelic_BAM_input/filtered_bam --fromBAM --bamExt '.filtered.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1315 ]; then exit 1 ; fi -WC=`mRNAseq -m allelic-mapping,deepTools_qc,alignment-free -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`mRNAseq -m allelic-mapping,deepTools_qc,alignment-free -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 3021 ]; then exit 1 ; fi #ncRNAseq -WC=`ncRNAseq -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ncRNAseq -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1269 ]; then exit 1 ; fi -WC=`ncRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ncRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1289 ]; then exit 1 ; fi -WC=`ncRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ncRNAseq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1131 ]; then exit 1 ; fi -WC=`ncRNAseq -i BAM_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ncRNAseq -i BAM_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 901 ]; then exit 1 ; fi #multiple comparison groups -WC=`ncRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ncRNAseq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1317 ]; then exit 1 ; fi # scRNAseq -#WC=`scRNAseq -i PE_input -o output --mode Gruen --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +#WC=`scRNAseq -i PE_input -o output --mode Gruen --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` #if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1038 ]; then exit 1 ; fi -#WC=`scRNAseq -i PE_input -o output --mode Gruen --snakemakeOptions " --dryrun --conda-prefix /tmp" --skipRaceID --splitLib .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +#WC=`scRNAseq -i PE_input -o output --mode Gruen --snakemakeOptions " --dryrun --conda-prefix /tmp" --skipRaceID --splitLib .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` #if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1015 ]; then exit 1 ; fi -WC=`scRNAseq -i PE_input -o output --mode STARsolo --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`scRNAseq -i PE_input -o output --mode STARsolo --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1642 ]; then exit 1 ; fi -WC=`scRNAseq -i PE_input -o output --mode STARsolo --skipVelocyto --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`scRNAseq -i PE_input -o output --mode STARsolo --skipVelocyto --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1467 ]; then exit 1 ; fi -WC=`scRNAseq -i PE_input -o output --mode Alevin --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`scRNAseq -i PE_input -o output --mode Alevin --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 714 ]; then exit 1 ; fi -WC=`scRNAseq -i PE_input -o output --mode Alevin --skipVelocyto --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`scRNAseq -i PE_input -o output --mode Alevin --skipVelocyto --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 604 ]; then exit 1 ; fi # WGBS -WC=`WGBS -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`WGBS -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1300 ]; then exit 1 ; fi -WC=`WGBS -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`WGBS -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1343 ]; then exit 1 ; fi -WC=`WGBS -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --aligner bwameth2 --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`WGBS -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --aligner bwameth2 --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1343 ]; then exit 1 ; fi -WC=`WGBS -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --GCbias .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`WGBS -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --GCbias .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1353 ]; then exit 1 ; fi -WC=`WGBS -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --fromBAM --snakemakeOptions " --dryrun --conda-prefix /tmp" --GCbias .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`WGBS -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --fromBAM --snakemakeOptions " --dryrun --conda-prefix /tmp" --GCbias .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 974 ]; then exit 1 ; fi -WC=`WGBS -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --fromBAM --fastqc --snakemakeOptions " --dryrun --conda-prefix /tmp" --GCbias .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`WGBS -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --fromBAM --fastqc --snakemakeOptions " --dryrun --conda-prefix /tmp" --GCbias .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 974 ]; then exit 1 ; fi -WC=`WGBS -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --fromBAM --skipBamQC --snakemakeOptions " --dryrun --conda-prefix /tmp" --GCbias .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`WGBS -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --fromBAM --skipBamQC --snakemakeOptions " --dryrun --conda-prefix /tmp" --GCbias .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 530 ]; then exit 1 ; fi # ATACseq -WC=`ATACseq -d BAM_input --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ATACseq -d BAM_input --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 460 ]; then exit 1 ; fi -WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 605 ]; then exit 1 ; fi -WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 706 ]; then exit 1 ; fi -WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller HMMRATAC .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller HMMRATAC .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 697 ]; then exit 1 ; fi -WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --maxFragmentSize 120 --qval 0.1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --maxFragmentSize 120 --qval 0.1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 605 ]; then exit 1 ; fi -WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1055 ]; then exit 1 ; fi #multicomp -WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 743 ]; then exit 1 ; fi -WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 860 ]; then exit 1 ; fi -WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller HMMRATAC .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller HMMRATAC .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 835 ]; then exit 1 ; fi -WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --maxFragmentSize 120 --qval 0.1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --maxFragmentSize 120 --qval 0.1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 743 ]; then exit 1 ; fi -WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`ATACseq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1193 ]; then exit 1 ; fi # HiC -WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --correctionMethod ICE .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --correctionMethod ICE .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 965 ]; then exit 1 ; fi -WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 891 ]; then exit 1 ; fi -WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 983 ]; then exit 1 ; fi -WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --enzyme DpnII .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --enzyme DpnII .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 891 ]; then exit 1 ; fi -WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --noTAD .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --noTAD .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 808 ]; then exit 1 ; fi -WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --aligner bwa-mem2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`HiC -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --aligner bwa-mem2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 891 ]; then exit 1 ; fi # preprocessing -WC=`preprocessing -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --fastqc --optDedupDist 2500 | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`preprocessing -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --fastqc --optDedupDist 2500 | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 761 ]; then exit 1 ; fi -WC=`preprocessing -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --fastqc --optDedupDist 2500 | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/host/d' | wc -l ` +WC=`preprocessing -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --fastqc --optDedupDist 2500 | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 761 ]; then exit 1 ; fi rm -rf SE_input PE_input BAM_input output allelic_input allelic_BAM_input /tmp/genes.gtf /tmp/genome.fa /tmp/genome.fa.fai /tmp/rmsk.txt /tmp/genes.bed /tmp/spikein_genes.gtf From 084c3e642ea7ba650be839ea78c859c4d9cc2467 Mon Sep 17 00:00:00 2001 From: "katarzyna.otylia.sikora@gmail.com" Date: Thu, 5 Sep 2024 14:00:43 +0200 Subject: [PATCH 05/35] fix 1023 --- snakePipes/shared/rules/umi_tools.snakefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/snakePipes/shared/rules/umi_tools.snakefile b/snakePipes/shared/rules/umi_tools.snakefile index 152ea6dec..8bdc569f3 100644 --- a/snakePipes/shared/rules/umi_tools.snakefile +++ b/snakePipes/shared/rules/umi_tools.snakefile @@ -86,7 +86,7 @@ else: elif not (aligner=="bwameth" or aligner=="bwameth2") : rule filter_reads: input: - bamfile = aligner+"/{sample}.bam" + bamfile = "filtered_bam/{sample}.filtered.tmp.bam" output: bamfile = "filtered_bam/{sample}.filtered.bam" shell: """ From c4d127c13743e8eb5da1c217328b3da7c4d2c4a8 Mon Sep 17 00:00:00 2001 From: "katarzyna.otylia.sikora@gmail.com" Date: Thu, 5 Sep 2024 14:11:00 +0200 Subject: [PATCH 06/35] fix test dag --- .ci_stuff/test_dag.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.ci_stuff/test_dag.sh b/.ci_stuff/test_dag.sh index d336a8fc3..f0cdbf636 100755 --- a/.ci_stuff/test_dag.sh +++ b/.ci_stuff/test_dag.sh @@ -189,9 +189,9 @@ if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1157 ]; then exit 1 ; fi WC=`DNAmapping -i SE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --dedup --properPairs | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1249 ]; then exit 1 ; fi WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --trim --aligner bwa | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` -if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1296 ]; then exit 1 ; fi +if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1388 ]; then exit 1 ; fi WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --trim --aligner bwa-mem2 | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` -if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1296 ]; then exit 1 ; fi +if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1388 ]; then exit 1 ; fi #allelic WC=`DNAmapping -m allelic-mapping -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l ` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2237 ]; then exit 1 ; fi From a7606877f67643dad2552d28630fc30b99a0e1e7 Mon Sep 17 00:00:00 2001 From: "katarzyna.otylia.sikora@gmail.com" Date: Thu, 5 Sep 2024 14:25:58 +0200 Subject: [PATCH 07/35] fix mRNAseq --- snakePipes/shared/rules/umi_tools.snakefile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/snakePipes/shared/rules/umi_tools.snakefile b/snakePipes/shared/rules/umi_tools.snakefile index 8bdc569f3..c69634fb6 100644 --- a/snakePipes/shared/rules/umi_tools.snakefile +++ b/snakePipes/shared/rules/umi_tools.snakefile @@ -73,7 +73,7 @@ if UMIDedup: {params.umitools_paired} {params.umitools_options} """ else: - if aligner == "Bowtie2": + if aligner == "Bowtie2" or aligner == "bwa" or aligner == "bwa-mem2": rule filter_reads: input: bamfile = "filtered_bam/{sample}.filtered.tmp.bam" @@ -83,10 +83,10 @@ else: mv {input.bamfile} {output.bamfile} """ - elif not (aligner=="bwameth" or aligner=="bwameth2") : + elif aligner == "STAR" or aligner == "HISAT2" : rule filter_reads: input: - bamfile = "filtered_bam/{sample}.filtered.tmp.bam" + bamfile = aligner + "/{sample}.bam" output: bamfile = "filtered_bam/{sample}.filtered.bam" shell: """ From 598a87a437e85d4008120674d1525c2fbd4af702 Mon Sep 17 00:00:00 2001 From: "katarzyna.otylia.sikora@gmail.com" Date: Thu, 5 Sep 2024 14:52:53 +0200 Subject: [PATCH 08/35] pytest --- tests/test_jobcounts.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_jobcounts.py b/tests/test_jobcounts.py index cffc110ce..e44b28746 100644 --- a/tests/test_jobcounts.py +++ b/tests/test_jobcounts.py @@ -474,7 +474,7 @@ def test_bwa(self, ifs): print(' '.join([str(i) for i in ci])) _p = sp.run(ci, capture_output=True, text=True) assert _p.returncode == 0 - assert parseSpOut(_p) == 143 + assert parseSpOut(_p) == 152 def test_bwa2(self, ifs): ci = [ "DNAmapping", @@ -493,7 +493,7 @@ def test_bwa2(self, ifs): print(' '.join([str(i) for i in ci])) _p = sp.run(ci, capture_output=True, text=True) assert _p.returncode == 0 - assert parseSpOut(_p) == 143 + assert parseSpOut(_p) == 152 def test_se(self, ifs): ci = [ "DNAmapping", From cda006541401231299bf008743fa1a87cdd1c86d Mon Sep 17 00:00:00 2001 From: "katarzyna.otylia.sikora@gmail.com" Date: Thu, 5 Sep 2024 15:19:07 +0200 Subject: [PATCH 09/35] fix 1025 --- snakePipes/shared/rules/ChIP_peak_calling.snakefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/snakePipes/shared/rules/ChIP_peak_calling.snakefile b/snakePipes/shared/rules/ChIP_peak_calling.snakefile index 2c1200e7f..da7ddeb2a 100755 --- a/snakePipes/shared/rules/ChIP_peak_calling.snakefile +++ b/snakePipes/shared/rules/ChIP_peak_calling.snakefile @@ -122,7 +122,7 @@ rule MACS2_peak_qc: # compute peak genome coverage peak_len=`awk '{{total+=$3-$2}}END{{print total}}' {params.peaks}` - genome_size=`awk '{{total+=$3-$2}}END{{print total}}' {params.genome_index}` + genome_size=`awk '{{total+=$3-$2}}END{{printf( "%14d",total) }}' {params.genome_index}` genomecov=`bc -l <<< "$peak_len/$genome_size"` # write peak-based QC metrics to output file From d73028305913e7a030a9243be7f75dcb48a66409 Mon Sep 17 00:00:00 2001 From: "katarzyna.otylia.sikora@gmail.com" Date: Mon, 9 Sep 2024 14:41:59 +0200 Subject: [PATCH 10/35] mRNAseq genome alias --- snakePipes/snakePipes.py | 11 +++++++++++ snakePipes/workflows/DNAmapping/Snakefile | 2 +- snakePipes/workflows/mRNAseq/Snakefile | 5 +++-- 3 files changed, 15 insertions(+), 3 deletions(-) diff --git a/snakePipes/snakePipes.py b/snakePipes/snakePipes.py index 63b49f6d1..5b867ecb7 100755 --- a/snakePipes/snakePipes.py +++ b/snakePipes/snakePipes.py @@ -381,6 +381,7 @@ def updateConfig(args): if args.configMode == "manual": d = { "snakemakeOptions": args.snakemakeOptions, + "snakemakeProfile": args.snakemakeProfile, "condaEnvDir": args.condaEnvDir, "organismsDir": args.organismsDir, "tempDir": args.tempDir, @@ -407,6 +408,16 @@ def updateConfig(args): sys.exit("Config file not found\n") updatedDict = cof.merge_dicts(currentDict, d) cof.write_configfile(os.path.join(baseDir, "shared", "defaults.yaml"), updatedDict) + + #update conda-prefix in snakemakeProfile + if args.condaEnvDir: + profilePath = cof.resolveSnakemakeProfile(d['snakemakeProfile'], baseDir) + f = open(profilePath / 'config.yaml') + pf = yaml.load(f, Loader=yaml.FullLoader) + pf['conda-prefix'] = args.condaEnvDir + cof.write_configfile(os.path.join(profilePath, "config.yaml"), pf) + f.close() + cof.load_configfile( os.path.join(baseDir, "shared", "defaults.yaml"), True, "Final Updated Config" ) diff --git a/snakePipes/workflows/DNAmapping/Snakefile b/snakePipes/workflows/DNAmapping/Snakefile index 579d10430..f5047efc3 100755 --- a/snakePipes/workflows/DNAmapping/Snakefile +++ b/snakePipes/workflows/DNAmapping/Snakefile @@ -63,7 +63,7 @@ if "allelic-mapping" in mode: SNPFile = "snp_genome/all_SNPs_" + strains[0] + "_" + genome_alias + ".txt.gz" elif len(strains) == 2: allele_hybrid = 'dual' - SNPFile = SNPFile = "snp_genome/all_" + strains[1] + "_SNPs_" + strains[0] + "_reference.based_on_" + genome_alias + ".txt" + SNPFile = "snp_genome/all_" + strains[1] + "_SNPs_" + strains[0] + "_reference.based_on_" + genome_alias + ".txt" include: os.path.join(maindir, "shared", "rules", "masked_genomeIndex.snakefile") elif allele_mode == 'map_only': diff --git a/snakePipes/workflows/mRNAseq/Snakefile b/snakePipes/workflows/mRNAseq/Snakefile index 9a914a587..d551b0f4b 100755 --- a/snakePipes/workflows/mRNAseq/Snakefile +++ b/snakePipes/workflows/mRNAseq/Snakefile @@ -52,15 +52,16 @@ if not fromBAM: ## Allele-specific JOBS if "allelic-mapping" in mode: + genome_alias = os.path.splitext(os.path.basename(genome))[0] # Updated global vars if mode = "allelic-mapping" if allele_mode == 'create_and_map': star_index_allelic = 'snp_genome/star_Nmasked/Genome' if len(strains) == 1: allele_hybrid = 'single' - SNPFile = "snp_genome/all_SNPs_" + strains[0] + "_" + genome + ".txt.gz" + SNPFile = "snp_genome/all_SNPs_" + strains[0] + "_" + genome_alias + ".txt.gz" elif len(strains) == 2: allele_hybrid = 'dual' - SNPFile = "snp_genome/all_" + strains[1] + "_SNPs_" + strains[0] + "_reference.based_on_" + genome + ".txt" + SNPFile = "snp_genome/all_" + strains[1] + "_SNPs_" + strains[0] + "_reference.based_on_" + genome_alias + ".txt" include: os.path.join(maindir, "shared", "rules", "masked_genomeIndex.snakefile") elif allele_mode == 'map_only': From 16e04bd2d03eda6000391a2100fd38e1e18dcfb0 Mon Sep 17 00:00:00 2001 From: "katarzyna.otylia.sikora@gmail.com" Date: Tue, 10 Sep 2024 11:47:34 +0200 Subject: [PATCH 11/35] fix snakePipes config --- snakePipes/snakePipes.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/snakePipes/snakePipes.py b/snakePipes/snakePipes.py index 5b867ecb7..6d358a5fa 100755 --- a/snakePipes/snakePipes.py +++ b/snakePipes/snakePipes.py @@ -103,6 +103,12 @@ def parse_arguments(): "in the workflow-specific yaml files and where conda is installed.", ) + configParser.add_argument( + "--snakemakeProfile", + help="Path to custom snakemake profile file.", + default=defaults["snakemakeProfile"] + ) + configParser.add_argument( "--organismsDir", help="The directory where global organism YAML files are to be stored. Both " From a2568b2fd77fb2ae51bc9ab48da5ea5ce9e6d6a2 Mon Sep 17 00:00:00 2001 From: "katarzyna.otylia.sikora@gmail.com" Date: Tue, 10 Sep 2024 12:14:47 +0200 Subject: [PATCH 12/35] docs --- docs/content/setting_up.rst | 4 ++-- docs/index.rst | 3 ++- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/docs/content/setting_up.rst b/docs/content/setting_up.rst index 697a150ed..d831ef54b 100644 --- a/docs/content/setting_up.rst +++ b/docs/content/setting_up.rst @@ -63,7 +63,7 @@ or for the pytests: Configuring snakePipes ---------------------- -Finally, at least one file (``defaults.yaml``) should be modified to match your compute infrastructure. The location of this file can be found out by executing: +Finally, config files ``defaults.yaml`` and snakemake profile should be modified to match your compute infrastructure. The location of this file can be found out by executing: .. code:: bash @@ -86,7 +86,7 @@ If you want to use the snakepipes_genericprofile, make sure to review the follow * ``module load slurm &&`` - could be omitted * ``resources.partition`` - set to your slurm partition - * ``conda-prefix`` - set to your preferred location where snakePipes environments should be stored + * ``conda-prefix`` - set to your preferred location where snakePipes environments should be stored. You can set this value by running `snakePipes config --condaEnvDir` and providing the respective path. * ``resources`` - make sure default resources make sense for your infrastructure * ``ccancel.sh`` - refers to the ccancel.sh file inside the profile directory and contains instructions on how to kill submitted jobs (on failure / interruption of snakemake). The module command could be omitted here as before diff --git a/docs/index.rst b/docs/index.rst index 32d6df5af..1773ada40 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -45,7 +45,8 @@ Quick start * Download genome fasta and annotations for an your organism, and build indexes, Check in :ref:`createIndices` -* Configure snakePipes with paths to organism and cluster configs on your system using snakePipes config. For detailed information, run: +* Configure snakePipes with paths to organism and snakemake configs on your system using snakePipes config. Importantly, take care to set `--condaEnvDir` parameter, which defaults to `/tmp`. + For detailed information, run: .. code:: bash From e3a7f51ef165d9b4c99f553ddb2b57ebc947050b Mon Sep 17 00:00:00 2001 From: WardDeb Date: Mon, 23 Sep 2024 15:23:09 +0200 Subject: [PATCH 13/35] drop log as omitted by profile --- snakePipes/shared/rules/split_bam_ops_ChIP_spikein.snakefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/snakePipes/shared/rules/split_bam_ops_ChIP_spikein.snakefile b/snakePipes/shared/rules/split_bam_ops_ChIP_spikein.snakefile index 7f3e33656..7cdd01aae 100755 --- a/snakePipes/shared/rules/split_bam_ops_ChIP_spikein.snakefile +++ b/snakePipes/shared/rules/split_bam_ops_ChIP_spikein.snakefile @@ -107,7 +107,7 @@ rule concatenate_scaling_factors: scale_factors_chip = "split_deepTools_qc/multiBamSummary/{part}.ChIP.scaling_factors.txt" output: "split_deepTools_qc/multiBamSummary/{part}.concatenated.scaling_factors.txt" shell: """ - cat {input.scale_factors_input} {input.scale_factors_chip} > {output} 2> {log} + cat {input.scale_factors_input} {input.scale_factors_chip} > {output} """ From e0b0c8a996ca6228087bb5aa602baed80ea19259 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Wed, 9 Oct 2024 11:01:25 +0200 Subject: [PATCH 14/35] drop default channel from makePairs env --- snakePipes/shared/defaults.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/snakePipes/shared/defaults.yaml b/snakePipes/shared/defaults.yaml index e6970966d..48006c547 100755 --- a/snakePipes/shared/defaults.yaml +++ b/snakePipes/shared/defaults.yaml @@ -5,7 +5,7 @@ ################################################################################ snakemakeOptions: '' organismsDir: 'shared/organisms' -snakemakeProfile: 'shared/profiles/local' +snakemakeProfile: 'shared/profiles/snakepipes_genericprofile' tempDir: /scratch/local # The following are only needed if you use the --emailAddress option smtpServer: @@ -19,4 +19,4 @@ max_thread: 25 #print tools versions toolsVersion: True oldConfig: -configMode: manual \ No newline at end of file +configMode: manual From 368c78f96efe8ee34c3c4b6693c735ef46a1ea53 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Wed, 9 Oct 2024 11:37:54 +0200 Subject: [PATCH 15/35] install test on py 3.13 too --- .github/workflows/linux.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/linux.yml b/.github/workflows/linux.yml index 49964a1a6..b9723025f 100644 --- a/.github/workflows/linux.yml +++ b/.github/workflows/linux.yml @@ -12,7 +12,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.11', '3.12'] + python-version: ['3.11', '3.12' ,'3.13'] optdeps: [".", ".[actions]", ".[docs]"] steps: - uses: actions/checkout@v4 From 89748e666dc7e8b4f17d35718b02537d3e91dd6f Mon Sep 17 00:00:00 2001 From: WardDeb Date: Wed, 9 Oct 2024 12:45:39 +0200 Subject: [PATCH 16/35] include docs for vcf index in makePairs wf, makePairs docs update --- docs/content/workflows/makePairs.rst | 4 ++-- snakePipes/parserCommon.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/content/workflows/makePairs.rst b/docs/content/workflows/makePairs.rst index b1e6ccba4..5ea102dd6 100644 --- a/docs/content/workflows/makePairs.rst +++ b/docs/content/workflows/makePairs.rst @@ -6,8 +6,8 @@ makePairs What it does ------------ -The snakePipes makePairs workflow allows users to process their HiC data from raw fastq files to HiC matrices in -an allele-specific manner. The workflow utilized mapping by bwa, followed by analysis +The snakePipes makePairs workflow allows users to process their HiC/uC data from raw fastq files to HiC matrices (in +an allele-specific manner). The workflow utilizes mapping by bwa, followed by analysis using `pairtools `__ . The workflow follows the `example workflow described in the documentation of pairtools `__ , which explains each step in detail and would be useful for new users to have a look at. Currently the output matrices are produced in the `.pairs `__ format. diff --git a/snakePipes/parserCommon.py b/snakePipes/parserCommon.py index 3508c8ce0..ecd8f5db7 100644 --- a/snakePipes/parserCommon.py +++ b/snakePipes/parserCommon.py @@ -139,7 +139,7 @@ def snpArguments(defaults): snpargs = parser.add_argument_group('Allele-specific mapping arguments') snpargs.add_argument("--VCFfile", default='', - help="VCF file to create N-masked genomes (default: 'None')") + help="VCF file to create N-masked genomes (default: 'None'). Note that for the makePairs workflow this file is assumed to be gzipped and indexed (with tabix).") snpargs.add_argument("--strains", default='', From 3426abf7d49436c5bb43633cbecfa1817f4b3dd0 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Wed, 9 Oct 2024 17:36:21 +0200 Subject: [PATCH 17/35] bulk makePairs implementation --- snakePipes/shared/rules/envs/makePairs.yaml | 2 +- snakePipes/shared/rules/pairtools.snakefile | 160 ++++++-------- .../shared/rules/pairtools_allelic.snakefile | 199 ++++++++++++++++++ snakePipes/workflows/makePairs/Snakefile | 43 +++- snakePipes/workflows/makePairs/defaults.yaml | 2 +- .../workflows/makePairs/internals.snakefile | 23 +- 6 files changed, 312 insertions(+), 117 deletions(-) create mode 100644 snakePipes/shared/rules/pairtools_allelic.snakefile diff --git a/snakePipes/shared/rules/envs/makePairs.yaml b/snakePipes/shared/rules/envs/makePairs.yaml index c470504fe..f270395e7 100644 --- a/snakePipes/shared/rules/envs/makePairs.yaml +++ b/snakePipes/shared/rules/envs/makePairs.yaml @@ -2,9 +2,9 @@ name: pairtools_phased channels: - conda-forge - bioconda - - defaults dependencies: - bwa + - cooler - samtools - tabix - bcftools diff --git a/snakePipes/shared/rules/pairtools.snakefile b/snakePipes/shared/rules/pairtools.snakefile index 95bb6c674..847ea3edd 100644 --- a/snakePipes/shared/rules/pairtools.snakefile +++ b/snakePipes/shared/rules/pairtools.snakefile @@ -1,70 +1,58 @@ -# based on https://github.com/caballero/snakemake-pairtools-phased/tree/df410ff +rule generate_chromsizes: + input: + genome_index + output: + 'genome/genome.chromsizes' + threads: 1 + shell:''' + cut -f1,2 {input} > {output} + ''' - -# Define function that returns pair files (phased or unphased), based on the reference. -def ret_pair(wildcards): - if "diploid_genome" in wildcards.ref: - # Phased setting - return f"pairs/{wildcards.sample}.{wildcards.ref}_phased.pairs.gz" - else: - return f"pairs/{wildcards.sample}.{wildcards.ref}.pairs.gz" - - -# different to bwa.snakefile -# here we skip the expensive sorting with samtools after bwa mem -# consider making this optional in bwa.snakefile rule bwa_mapping: input: fq1="FASTQ_fastp/{sample}_R1.fastq.gz", - fq2="FASTQ_fastp/{sample}_R2.fastq.gz", - ix="genome/{ref}.fa.gz.bwt", + fq2="FASTQ_fastp/{sample}_R2.fastq.gz" output: - bam="bam/{sample}.{ref}.bam", + bam="bam/{sample}.bam", threads: 30 params: - bwathreads=config["alignerThreads"], bwaparams=config["alignerOptions"], - fna=lambda wildcards, input: Path(input.ix).with_suffix(""), + bwa_index = bwa_index resources: mem_mb=3000, benchmark: - "bam/.benchmark/bwa_mapping.{sample}.{ref}.benchmark" + "bam/.benchmark/bwa_mapping.{sample}.benchmark" conda: CONDA_MAKEPAIRS_ENV shell: """ bwa mem \ {params.bwaparams} \ - -t {params.bwathreads} \ - {params.fna} \ + -t 22 \ + {params.bwa_index} \ {input.fq1} \ {input.fq2} \ | samtools view -@ 8 -b \ > {output.bam} """ - rule pairtools_parse: input: - bam="bam/{sample}.{ref}.bam", - chr_sizes="genome/{ref}.chromsizes", + bam="bam/{sample}.bam", + chr_sizes='genome/genome.chromsizes' output: - pairs="pairs/{sample}.{ref}.pairs.gz", + pairs=temp("pairs/{sample}.unsorted.pairs.gz"), params: - minmapq=40, - cols=lambda wildcards: ( - "--add-columns XB,AS,XS" if "diploid_genome" in wildcards.ref else "" - ), + minmapq=40 threads: 12 benchmark: - "pairs/.benchmark/pairtools_parse.{sample}.{ref}.benchmark" + "pairs/.benchmark/pairtools_parse.{sample}.benchmark" conda: CONDA_MAKEPAIRS_ENV shell: """ pairtools parse \ --min-mapq {params.minmapq} \ - {params.cols} \ --drop-sam \ --walks-policy 5unique \ -c {input.chr_sizes} \ @@ -72,69 +60,39 @@ rule pairtools_parse: -o {output.pairs} """ - -rule pairtools_phase: - input: - pairs="pairs/{sample}.diploid_genome.pairs.gz", - output: - pairs="pairs/{sample}.diploid_genome_phased.pairs.gz", - params: - hap1=strains[0], - hap2=strains[1], - threads: 12 - benchmark: - "pairs/.benchmark/pairtools_phase.{sample}.benchmark" - conda: - CONDA_MAKEPAIRS_ENV - shell: - """ - pairtools phase \ - --phase-suffixes _{params.hap1} _{params.hap2} \ - --tag-mode XB \ - --clean-output \ - {input.pairs} -o {output.pairs} - """ - - rule pairtools_sort: input: - ret_pair, + pairs = "pairs/{sample}.unsorted.pairs.gz", output: - pairs="pairs/{sample}.{ref}.pairs.sorted.gz", + pairs = "pairs/{sample}.pairs.gz", threads: 20 benchmark: - "pairs/.benchmark/pairtools_sort.{sample}.{ref}.benchmark" + "pairs/.benchmark/pairtools_sort.{sample}.benchmark" conda: CONDA_MAKEPAIRS_ENV shell: """ pairtools sort \ - {input} \ + {input.pairs} \ -o {output.pairs} \ --memory 20G """ - rule pairtools_dedup: input: - pairs="pairs/{sample}.{ref}.pairs.sorted.gz", + pairs="pairs/{sample}.pairs.gz", output: - pairs="pairs/{sample}.{ref}.pairs.dedup.gz", - stats="pairs/{sample}.{ref}.pairs.dedup.stats", - params: - extra_cols=lambda wildcards: ( - "--extra-col-pair phase1 phase2" if "diploid" in wildcards.ref else "" - ), + pairs="pairs/{sample}.pairs.dedup.gz", + stats="pairs/{sample}.pairs.dedup.stats" threads: 12 benchmark: - "pairs/.benchmark/pairtools_dedup.{sample}.{ref}.benchmark" + "pairs/.benchmark/pairtools_dedup.{sample}.benchmark" conda: CONDA_MAKEPAIRS_ENV shell: """ pairtools dedup \ --mark-dups \ - {params.extra_cols} \ --output-dups - \ --output-unmapped - \ --output-stats {output.stats} \ @@ -142,42 +100,53 @@ rule pairtools_dedup: {input.pairs} """ +rule pairix: + input: + pairs = 'pairs/{sample}.pairs.dedup.gz' + output: + ix = 'pairs/{sample}.pairs.dedup.gz.px2' + threads: 2 + conda: + CONDA_MAKEPAIRS_ENV + shell: + """ + pairix -f -p pairs {input.pairs} + """ -rule pairtools_filter_phased: +rule cooler: input: - pairs="pairs/{sample}.diploid_genome.pairs.dedup.gz", + pairs = 'pairs/{sample}.pairs.dedup.gz', + ix = 'pairs/{sample}.pairs.dedup.gz.px2', + chromsizes = 'genome/genome.chromsizes' output: - stats="phase_stats/{sample}.diploid_genome_{phasetype}.pairs.stats", - pairs="phase_stats/{sample}.diploid_genome_{phasetype}.pairs.gz", - params: - filterparam=lambda wildcards: PHASEDIC[wildcards.phasetype], - resources: - mem_mb=1000, - benchmark: - "phase_stats/.benchmark/pairtools_filter_phased.{sample}.diploid_genome_{phasetype}.benchmark" - threads: 12 + cool = 'cooler/{sample}.5000.cool' + threads: 20 conda: CONDA_MAKEPAIRS_ENV shell: """ - pairtools select \ - '{params.filterparam}' \ - {input.pairs} \ - -o {output.pairs} - pairtools stats {output.pairs} -o {output.stats} + cooler cload pairix -p {threads} {input.chromsizes}:5000 {input.pairs} {output.cool} + cooler balance --nproc {threads} {output.cool} """ +rule mcool: + input: + cool = 'cooler/{sample}.5000.cool' + output: + mcool = 'cooler/{sample}.5000.mcool' + threads: 20 + conda: + CONDA_MAKEPAIRS_ENV + shell: + """ + cooler zoomify --resolutions 5000,10000,20000,40000,80000,120000 --balance --nproc {threads} {input.cool} + """ rule multiqc: input: - stats=expand( - "pairs/{sample}.{ref}.pairs.dedup.stats", sample=samples, ref=REFERENCES - ), - phasedstats=expand( - "phase_stats/{sample}.diploid_genome_{phasetype}.pairs.stats", - sample=samples, - phasetype=PHASEDIC.keys(), - ), + cools=expand( + 'cooler/{sample}.5000.mcool', sample=samples + ) output: html="multiqc/multiqc_report.html", params: @@ -189,11 +158,10 @@ rule multiqc: CONDA_MAKEPAIRS_ENV shell: """ - echo input: {input.phasedstats} multiqc \ --module pairtools \ --module fastqc \ --module fastp \ -o {params.odir} \ . - """ + """ \ No newline at end of file diff --git a/snakePipes/shared/rules/pairtools_allelic.snakefile b/snakePipes/shared/rules/pairtools_allelic.snakefile new file mode 100644 index 000000000..95bb6c674 --- /dev/null +++ b/snakePipes/shared/rules/pairtools_allelic.snakefile @@ -0,0 +1,199 @@ +# based on https://github.com/caballero/snakemake-pairtools-phased/tree/df410ff + + +# Define function that returns pair files (phased or unphased), based on the reference. +def ret_pair(wildcards): + if "diploid_genome" in wildcards.ref: + # Phased setting + return f"pairs/{wildcards.sample}.{wildcards.ref}_phased.pairs.gz" + else: + return f"pairs/{wildcards.sample}.{wildcards.ref}.pairs.gz" + + +# different to bwa.snakefile +# here we skip the expensive sorting with samtools after bwa mem +# consider making this optional in bwa.snakefile +rule bwa_mapping: + input: + fq1="FASTQ_fastp/{sample}_R1.fastq.gz", + fq2="FASTQ_fastp/{sample}_R2.fastq.gz", + ix="genome/{ref}.fa.gz.bwt", + output: + bam="bam/{sample}.{ref}.bam", + threads: 30 + params: + bwathreads=config["alignerThreads"], + bwaparams=config["alignerOptions"], + fna=lambda wildcards, input: Path(input.ix).with_suffix(""), + resources: + mem_mb=3000, + benchmark: + "bam/.benchmark/bwa_mapping.{sample}.{ref}.benchmark" + conda: + CONDA_MAKEPAIRS_ENV + shell: + """ + bwa mem \ + {params.bwaparams} \ + -t {params.bwathreads} \ + {params.fna} \ + {input.fq1} \ + {input.fq2} \ + | samtools view -@ 8 -b \ + > {output.bam} + """ + + +rule pairtools_parse: + input: + bam="bam/{sample}.{ref}.bam", + chr_sizes="genome/{ref}.chromsizes", + output: + pairs="pairs/{sample}.{ref}.pairs.gz", + params: + minmapq=40, + cols=lambda wildcards: ( + "--add-columns XB,AS,XS" if "diploid_genome" in wildcards.ref else "" + ), + threads: 12 + benchmark: + "pairs/.benchmark/pairtools_parse.{sample}.{ref}.benchmark" + conda: + CONDA_MAKEPAIRS_ENV + shell: + """ + pairtools parse \ + --min-mapq {params.minmapq} \ + {params.cols} \ + --drop-sam \ + --walks-policy 5unique \ + -c {input.chr_sizes} \ + {input.bam} \ + -o {output.pairs} + """ + + +rule pairtools_phase: + input: + pairs="pairs/{sample}.diploid_genome.pairs.gz", + output: + pairs="pairs/{sample}.diploid_genome_phased.pairs.gz", + params: + hap1=strains[0], + hap2=strains[1], + threads: 12 + benchmark: + "pairs/.benchmark/pairtools_phase.{sample}.benchmark" + conda: + CONDA_MAKEPAIRS_ENV + shell: + """ + pairtools phase \ + --phase-suffixes _{params.hap1} _{params.hap2} \ + --tag-mode XB \ + --clean-output \ + {input.pairs} -o {output.pairs} + """ + + +rule pairtools_sort: + input: + ret_pair, + output: + pairs="pairs/{sample}.{ref}.pairs.sorted.gz", + threads: 20 + benchmark: + "pairs/.benchmark/pairtools_sort.{sample}.{ref}.benchmark" + conda: + CONDA_MAKEPAIRS_ENV + shell: + """ + pairtools sort \ + {input} \ + -o {output.pairs} \ + --memory 20G + """ + + +rule pairtools_dedup: + input: + pairs="pairs/{sample}.{ref}.pairs.sorted.gz", + output: + pairs="pairs/{sample}.{ref}.pairs.dedup.gz", + stats="pairs/{sample}.{ref}.pairs.dedup.stats", + params: + extra_cols=lambda wildcards: ( + "--extra-col-pair phase1 phase2" if "diploid" in wildcards.ref else "" + ), + threads: 12 + benchmark: + "pairs/.benchmark/pairtools_dedup.{sample}.{ref}.benchmark" + conda: + CONDA_MAKEPAIRS_ENV + shell: + """ + pairtools dedup \ + --mark-dups \ + {params.extra_cols} \ + --output-dups - \ + --output-unmapped - \ + --output-stats {output.stats} \ + -o {output.pairs} \ + {input.pairs} + """ + + +rule pairtools_filter_phased: + input: + pairs="pairs/{sample}.diploid_genome.pairs.dedup.gz", + output: + stats="phase_stats/{sample}.diploid_genome_{phasetype}.pairs.stats", + pairs="phase_stats/{sample}.diploid_genome_{phasetype}.pairs.gz", + params: + filterparam=lambda wildcards: PHASEDIC[wildcards.phasetype], + resources: + mem_mb=1000, + benchmark: + "phase_stats/.benchmark/pairtools_filter_phased.{sample}.diploid_genome_{phasetype}.benchmark" + threads: 12 + conda: + CONDA_MAKEPAIRS_ENV + shell: + """ + pairtools select \ + '{params.filterparam}' \ + {input.pairs} \ + -o {output.pairs} + pairtools stats {output.pairs} -o {output.stats} + """ + + +rule multiqc: + input: + stats=expand( + "pairs/{sample}.{ref}.pairs.dedup.stats", sample=samples, ref=REFERENCES + ), + phasedstats=expand( + "phase_stats/{sample}.diploid_genome_{phasetype}.pairs.stats", + sample=samples, + phasetype=PHASEDIC.keys(), + ), + output: + html="multiqc/multiqc_report.html", + params: + odir="multiqc", + benchmark: + "multiqc/.benchmark/multiqc.benchmark" + threads: 1 + conda: + CONDA_MAKEPAIRS_ENV + shell: + """ + echo input: {input.phasedstats} + multiqc \ + --module pairtools \ + --module fastqc \ + --module fastp \ + -o {params.odir} \ + . + """ diff --git a/snakePipes/workflows/makePairs/Snakefile b/snakePipes/workflows/makePairs/Snakefile index a02ee6331..186f014e8 100644 --- a/snakePipes/workflows/makePairs/Snakefile +++ b/snakePipes/workflows/makePairs/Snakefile @@ -30,22 +30,41 @@ include: os.path.join(maindir, "shared", "rules", "FASTQ.snakefile") # FastQC if fastqc: - include: os.path.join(maindir, "shared", "rules", "FastQC.snakefile") # trimming if trim: - include: os.path.join(maindir, "shared", "rules", "trimming.snakefile") # umi_tools: needed for FASTQ handling include: os.path.join(maindir, "shared", "rules", "umi_tools.snakefile") -# diploid_genome: concatenation and indexing -include: os.path.join(maindir, "shared", "rules", "diploid_genome.snakefile") -# pairtools: bwa mapping (without sorting), pairtools rules & multiqc -include: os.path.join(maindir, "shared", "rules", "pairtools.snakefile") + + + +# Decision to run allelic mode or not is made on the VCFfile arguments + strains argument +ALLELICMODE = False +if config['VCFfile']: + # VCFfile set, assert strains are there: + if config['strains']: + ALLELICMODE = True + # If no alignerOpts are set, set default for Xb parsing: + if not config['alignerOptions']: + config['alignerOptions'] = '-SPu -T0' + # Generation of diploid genome (bwa) + include: os.path.join(maindir, "shared", "rules", "diploid_genome.snakefile") + # pairtools: bwa mapping (without sorting), pairtools rules & multiqc + include: os.path.join(maindir, "shared", "rules", "pairtools_allelic.snakefile") + else: + if not config['alignerOptions']: + config['alignerOptions'] = '-SP -T0' + include: os.path.join(maindir, "shared", "rules", "pairtools.snakefile") +else: + if not config['alignerOptions']: + config['alignerOptions'] = '-SP -T0' + include: os.path.join(maindir, "shared", "rules", "pairtools.snakefile") + def run_FastQC(fastqc): @@ -70,6 +89,15 @@ def run_Trimming(trim, fastqc): return [] +def run_Pairtools(ALLELICMODE): + if ALLELICMODE: + return([ + "genome/diploid_genome.chromsizes", + "multiqc/multiqc_report.html" + ]) + else: + return expand("pairs/{sample}.pairs.dedup.gz", sample=samples) + ### execute before workflow starts ############################################# # does NOT seem to execute "onstart" ################################################################################ @@ -108,8 +136,7 @@ rule all: expand("originalFASTQ/{sample}{read}.fastq.gz", sample=samples, read=reads), run_FastQC(fastqc), run_Trimming(trim, fastqc), - "genome/diploid_genome.chromsizes", - "multiqc/multiqc_report.html", + "multiqc/multiqc_report.html" ### execute after workflow finished ############################################ diff --git a/snakePipes/workflows/makePairs/defaults.yaml b/snakePipes/workflows/makePairs/defaults.yaml index 7f51a043e..062d233a7 100644 --- a/snakePipes/workflows/makePairs/defaults.yaml +++ b/snakePipes/workflows/makePairs/defaults.yaml @@ -32,7 +32,7 @@ UMIDedupOpts: "_" plotFormat: png bwBinSize: 1000 aligner: 'bwa' -alignerOptions: '-SPu -T0' +alignerOptions: alignerThreads: 30 fromBAM: False diff --git a/snakePipes/workflows/makePairs/internals.snakefile b/snakePipes/workflows/makePairs/internals.snakefile index 7f30e121d..1ecde130c 100644 --- a/snakePipes/workflows/makePairs/internals.snakefile +++ b/snakePipes/workflows/makePairs/internals.snakefile @@ -14,7 +14,6 @@ if trim: ## genome names for allele-sp mapping -strains = list(map(str.strip, re.split(",|;", config["strains"]))) infiles = sorted(glob.glob(os.path.join(str(indir or ""), "*" + ext))) @@ -28,13 +27,15 @@ del infiles REFERENCES = ["diploid_genome"] # possible phasetypes of contacts -PHASETYPES = [strains[0], strains[1], "unphased", "trans"] - -PHASEFILTER = [ - '(phase1=="0") and (phase2=="0")', - '(phase1=="1") and (phase2=="1")', - '(phase1==".") or (phase2==".")', - '(phase1!=phase2) and (phase1!=".") and (phase2!=".") and (phase1!="!") and (phase2!="!")', -] - -PHASEDIC = dict(map(lambda i, j: (i, j), PHASETYPES, PHASEFILTER)) +if config['strains']: + strains = list(map(str.strip, re.split(",|;", config["strains"]))) + PHASETYPES = [strains[0], strains[1], "unphased", "trans"] + + PHASEFILTER = [ + '(phase1=="0") and (phase2=="0")', + '(phase1=="1") and (phase2=="1")', + '(phase1==".") or (phase2==".")', + '(phase1!=phase2) and (phase1!=".") and (phase2!=".") and (phase1!="!") and (phase2!="!")', + ] + + PHASEDIC = dict(map(lambda i, j: (i, j), PHASETYPES, PHASEFILTER)) From 1eccad2516965fc92068ba41a567e789ac8bdcf2 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Wed, 9 Oct 2024 17:36:51 +0200 Subject: [PATCH 18/35] v3.0.1 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 168ec77d0..4cf34f3ce 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta" name = "snakePipes" description = 'Snakemake workflows and wrappers for NGS data processing from the MPI-IE' readme = "README.md" -version = "3.0.0" +version = "3.0.1" keywords = [ "DNAmapping", "ChIPSeq", From 54f74511b6c90b607e5527b15d658c1873224c55 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Wed, 9 Oct 2024 17:39:25 +0200 Subject: [PATCH 19/35] revert defaults to local profile --- snakePipes/shared/defaults.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/snakePipes/shared/defaults.yaml b/snakePipes/shared/defaults.yaml index 48006c547..f5de896e0 100755 --- a/snakePipes/shared/defaults.yaml +++ b/snakePipes/shared/defaults.yaml @@ -5,7 +5,7 @@ ################################################################################ snakemakeOptions: '' organismsDir: 'shared/organisms' -snakemakeProfile: 'shared/profiles/snakepipes_genericprofile' +snakemakeProfile: 'shared/profiles/local' tempDir: /scratch/local # The following are only needed if you use the --emailAddress option smtpServer: From c069a520c9ce0c720bd7a98062fbfb7b791037ec Mon Sep 17 00:00:00 2001 From: WardDeb Date: Wed, 9 Oct 2024 17:55:02 +0200 Subject: [PATCH 20/35] set version in conda-recipe too --- conda-recipe/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml index 77afba14c..775a1a5e8 100755 --- a/conda-recipe/meta.yaml +++ b/conda-recipe/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "3.0.0" %} +{% set version = "3.0.1" %} package: name: snakepipes From d3636a54d6beda86f70edafbe6b9a0ba1d467638 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Wed, 9 Oct 2024 18:10:03 +0200 Subject: [PATCH 21/35] docs fix theme --- docs/conf.py | 2 +- docs/content/News.rst | 14 ++++++++++++++ 2 files changed, 15 insertions(+), 1 deletion(-) diff --git a/docs/conf.py b/docs/conf.py index 3a0ab11de..8128a6d03 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -150,7 +150,7 @@ # import them both locally and on rtd html_theme = 'sphinx_rtd_theme' # 'alabaster' 'sphinx_rtd_theme' -html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] +# html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] # deprecated # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the diff --git a/docs/content/News.rst b/docs/content/News.rst index 933e6fc00..cc387784d 100644 --- a/docs/content/News.rst +++ b/docs/content/News.rst @@ -1,6 +1,20 @@ snakePipes News =============== +snakePipes 3.0.1 +________________ + + * installation test for python 3.13 + * bulk mode in makePairs wf + +snakePipes 3.0.0 +________________ + +* clusteryaml omitted for profiles +* All workflows have '-' removed from their name +* toml file installation +* makePairs mode introduced + snakePipes 2.9.0 ________________ From 7eba06130a5758a3a1939c3a116315eaba0afbdd Mon Sep 17 00:00:00 2001 From: WardDeb Date: Wed, 9 Oct 2024 18:16:05 +0200 Subject: [PATCH 22/35] setuptools in conda recipe ? --- conda-recipe/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml index 775a1a5e8..00a6e19db 100755 --- a/conda-recipe/meta.yaml +++ b/conda-recipe/meta.yaml @@ -17,6 +17,7 @@ requirements: - python >=3 - pip - seaborn + - setuptools run: - python >=3.11 - snakemake >=8 From 37f8434af803b28d87cd6d868b8fcac8767b9878 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Wed, 9 Oct 2024 18:17:14 +0200 Subject: [PATCH 23/35] lint conf.py --- docs/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/conf.py b/docs/conf.py index 8128a6d03..4d561425c 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -150,7 +150,7 @@ # import them both locally and on rtd html_theme = 'sphinx_rtd_theme' # 'alabaster' 'sphinx_rtd_theme' -# html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] # deprecated +# html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the From 6c19df353f1cb27a68230ddbd991647f81134604 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Wed, 9 Oct 2024 18:21:55 +0200 Subject: [PATCH 24/35] drop unused import --- docs/conf.py | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/conf.py b/docs/conf.py index 4d561425c..a0d0e1939 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -15,7 +15,6 @@ import sys import os from importlib.metadata import version as importlibversion -import sphinx_rtd_theme # to allow readthedocs to compile without installing some dependencies import mock From 693cfff8aaa49f1c3aea79bcbb62e30a95011a89 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Wed, 9 Oct 2024 19:29:00 +0200 Subject: [PATCH 25/35] pin host python conda recipe < 3.13 --- conda-recipe/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml index 00a6e19db..68e41ad5e 100755 --- a/conda-recipe/meta.yaml +++ b/conda-recipe/meta.yaml @@ -14,7 +14,7 @@ build: requirements: host: - - python >=3 + - python >=3, < 3.13 - pip - seaborn - setuptools From 017189544428846b7f92ed2dcf45a0ca327d3abb Mon Sep 17 00:00:00 2001 From: WardDeb Date: Wed, 9 Oct 2024 21:07:17 +0200 Subject: [PATCH 26/35] properly set subdir to use osx-64, increase verbosity on conda env create command --- .github/workflows/osx.yml | 2 +- snakePipes/snakePipes.py | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/osx.yml b/.github/workflows/osx.yml index e08831e48..667c9e168 100644 --- a/.github/workflows/osx.yml +++ b/.github/workflows/osx.yml @@ -46,6 +46,6 @@ jobs: pip install . - name: createEnvsOSX run: | - conda config --add subdirs osx-64 + conda config --set subdir osx-64 snakePipes createEnvs --only ${{matrix.envs}} diff --git a/snakePipes/snakePipes.py b/snakePipes/snakePipes.py index 6d358a5fa..7240ad91d 100755 --- a/snakePipes/snakePipes.py +++ b/snakePipes/snakePipes.py @@ -347,6 +347,7 @@ def createCondaEnvs(args): if not args.info: if not os.path.exists(os.path.join(condaEnvDir, h)): print(f"Creating environment ({envNum}/{numberEnvs}) from {env} with hash {h}") + print(f"Actual command: {' '.join(cmd)}") try: os.makedirs(os.path.join(condaEnvDir, h), exist_ok=True) subprocess.check_call(cmd) From bd32a8053bf2dfc95048a52dd55ad19dc1afa908 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Thu, 10 Oct 2024 12:27:56 +0200 Subject: [PATCH 27/35] pep approved classifiers --- pyproject.toml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 4cf34f3ce..50368c875 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -24,8 +24,7 @@ authors = [ ] classifiers = [ - "Intended Audience :: Bioinformaticians", - "Intended Audience :: Biologists", + "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Programming Language :: Python :: 3", ] From 8e5550deff77e87750e514be8a7e27b4bed15196 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Thu, 10 Oct 2024 13:41:02 +0200 Subject: [PATCH 28/35] keep multiQC output consistent with other workflows --- snakePipes/shared/rules/pairtools.snakefile | 6 +++--- snakePipes/shared/rules/pairtools_allelic.snakefile | 6 +++--- snakePipes/workflows/makePairs/Snakefile | 11 +---------- 3 files changed, 7 insertions(+), 16 deletions(-) diff --git a/snakePipes/shared/rules/pairtools.snakefile b/snakePipes/shared/rules/pairtools.snakefile index 847ea3edd..a22392b52 100644 --- a/snakePipes/shared/rules/pairtools.snakefile +++ b/snakePipes/shared/rules/pairtools.snakefile @@ -148,11 +148,11 @@ rule multiqc: 'cooler/{sample}.5000.mcool', sample=samples ) output: - html="multiqc/multiqc_report.html", + html="multiQC/multiqc_report.html", params: - odir="multiqc", + odir="multiQC", benchmark: - "multiqc/.benchmark/multiqc.benchmark" + "multiQC/.benchmark/multiqc.benchmark" threads: 1 conda: CONDA_MAKEPAIRS_ENV diff --git a/snakePipes/shared/rules/pairtools_allelic.snakefile b/snakePipes/shared/rules/pairtools_allelic.snakefile index 95bb6c674..6648de95f 100644 --- a/snakePipes/shared/rules/pairtools_allelic.snakefile +++ b/snakePipes/shared/rules/pairtools_allelic.snakefile @@ -179,11 +179,11 @@ rule multiqc: phasetype=PHASEDIC.keys(), ), output: - html="multiqc/multiqc_report.html", + html="multiQC/multiqc_report.html", params: - odir="multiqc", + odir="multiQC", benchmark: - "multiqc/.benchmark/multiqc.benchmark" + "multiQC/.benchmark/multiqc.benchmark" threads: 1 conda: CONDA_MAKEPAIRS_ENV diff --git a/snakePipes/workflows/makePairs/Snakefile b/snakePipes/workflows/makePairs/Snakefile index 186f014e8..c87d836ff 100644 --- a/snakePipes/workflows/makePairs/Snakefile +++ b/snakePipes/workflows/makePairs/Snakefile @@ -89,15 +89,6 @@ def run_Trimming(trim, fastqc): return [] -def run_Pairtools(ALLELICMODE): - if ALLELICMODE: - return([ - "genome/diploid_genome.chromsizes", - "multiqc/multiqc_report.html" - ]) - else: - return expand("pairs/{sample}.pairs.dedup.gz", sample=samples) - ### execute before workflow starts ############################################# # does NOT seem to execute "onstart" ################################################################################ @@ -136,7 +127,7 @@ rule all: expand("originalFASTQ/{sample}{read}.fastq.gz", sample=samples, read=reads), run_FastQC(fastqc), run_Trimming(trim, fastqc), - "multiqc/multiqc_report.html" + "multiQC/multiqc_report.html" ### execute after workflow finished ############################################ From cf2d4fe89f1b46de4aa2c8bbbe5449b4f566742a Mon Sep 17 00:00:00 2001 From: WardDeb Date: Fri, 11 Oct 2024 09:20:36 +0200 Subject: [PATCH 29/35] v3.1.0, not 3.0.1 --- conda-recipe/meta.yaml | 2 +- docs/content/News.rst | 2 +- pyproject.toml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml index 68e41ad5e..533b373c5 100755 --- a/conda-recipe/meta.yaml +++ b/conda-recipe/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "3.0.1" %} +{% set version = "3.1.0" %} package: name: snakepipes diff --git a/docs/content/News.rst b/docs/content/News.rst index cc387784d..f6e5eeead 100644 --- a/docs/content/News.rst +++ b/docs/content/News.rst @@ -1,7 +1,7 @@ snakePipes News =============== -snakePipes 3.0.1 +snakePipes 3.1.0 ________________ * installation test for python 3.13 diff --git a/pyproject.toml b/pyproject.toml index 50368c875..69d09d8f4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta" name = "snakePipes" description = 'Snakemake workflows and wrappers for NGS data processing from the MPI-IE' readme = "README.md" -version = "3.0.1" +version = "3.1.0" keywords = [ "DNAmapping", "ChIPSeq", From 06581571d7b5ce9101bb29b9005494935d2db52d Mon Sep 17 00:00:00 2001 From: WardDeb Date: Tue, 22 Oct 2024 14:14:11 +0200 Subject: [PATCH 30/35] drop --userYAML in createIndices --- snakePipes/workflows/createIndices/Snakefile | 15 +++++++++------ .../workflows/createIndices/createIndices.py | 4 ---- 2 files changed, 9 insertions(+), 10 deletions(-) diff --git a/snakePipes/workflows/createIndices/Snakefile b/snakePipes/workflows/createIndices/Snakefile index 94af0085e..8384ec0f5 100755 --- a/snakePipes/workflows/createIndices/Snakefile +++ b/snakePipes/workflows/createIndices/Snakefile @@ -171,12 +171,15 @@ onsuccess: f = open(os.path.join(outdir, "genome_fasta", "effectiveSize")) organismDictionary['genome_size'] = int(float(f.read().strip())) f.close() - if not userYAML: - yamlPath = os.path.join(maindir, organismsDir, "{}.yaml".format(genome)) - else: - yamlPath = os.path.join(outdir, "{}.yaml".format(genome)) - print("Storing the organism YAML file in {}".format(yamlPath)) - cf.write_configfile(yamlPath, organismDictionary) + orgDir_yamlPath = os.path.join(maindir, organismsDir, f"{genome}.yaml") + outDir_yamlPath = os.path.join(outdir, f"{genome}.yaml") + try: + cf.write_configfile(orgDir_yamlPath, organismDictionary) + print(f"{genome} yaml written to {orgDir_yamlPath}") + except (PermissionError, FileNotFoundError) as e: + print(f"Error writing in the organism dir {e}") + cf.write_configfile(outDir_yamlPath, organismDictionary) + print(f"{genome} yaml written to {outDir_yamlPath}") if "verbose" in config and config["verbose"]: print("\n--- index creation workflow finished successfully! --------------------------------\n") diff --git a/snakePipes/workflows/createIndices/createIndices.py b/snakePipes/workflows/createIndices/createIndices.py index f9ef8212e..36e02e733 100755 --- a/snakePipes/workflows/createIndices/createIndices.py +++ b/snakePipes/workflows/createIndices/createIndices.py @@ -77,10 +77,6 @@ def parse_args(defaults={"configFile": None, "clusterConfigFile": None, optional.add_argument("--rmskURL", help="URL or local path to where the repeat masker output file is located. This is only required if you plan to run the ncRNAseq workflow.") - optional.add_argument("--userYAML", - action="store_true", - help="By default, this workflow creates an organism YAML file where snakePipes will look for it by default. If this isn't desired (e.g., you don't want the organism to be selectable by default or you don't have write permissions to the snakePipes installation) you can specify this option and the YAML file will instead be created in the location specified by the `-o` option.") - optional.add_argument("--salmonIndexOptions", help="Options to pass to salmon for index creation.", default=defaults["salmonIndexOptions"]) From 115e3d9e51cb5425da0a16034095b0514051462e Mon Sep 17 00:00:00 2001 From: WardDeb Date: Tue, 22 Oct 2024 14:15:23 +0200 Subject: [PATCH 31/35] news --- docs/content/News.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/content/News.rst b/docs/content/News.rst index f6e5eeead..032f9678a 100644 --- a/docs/content/News.rst +++ b/docs/content/News.rst @@ -6,6 +6,7 @@ ________________ * installation test for python 3.13 * bulk mode in makePairs wf + * Removal of --user flag in createIndices. Organism yamls are by default written to both installation folder and output folder. snakePipes 3.0.0 ________________ From daeede6a270a67771ecc60a5967bbe88ed0f669c Mon Sep 17 00:00:00 2001 From: WardDeb Date: Tue, 22 Oct 2024 14:31:33 +0200 Subject: [PATCH 32/35] fq in conda-forge != fq in bioconda --- snakePipes/shared/rules/envs/shared.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/snakePipes/shared/rules/envs/shared.yaml b/snakePipes/shared/rules/envs/shared.yaml index fcf45b73e..f4f0af652 100755 --- a/snakePipes/shared/rules/envs/shared.yaml +++ b/snakePipes/shared/rules/envs/shared.yaml @@ -15,6 +15,6 @@ dependencies: - multiqc = 1.23 - fastp = 0.23.4 - umi_tools = 1.1.4 - - fq = 0.11.0 + - bioconda::fq = 0.13.0 - pybigwig = 0.3.22 From 1803dfa5e89acc92f9cf30005f94d935d85aa2a7 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Tue, 22 Oct 2024 14:35:25 +0200 Subject: [PATCH 33/35] pin fq to 0.12.0 for osx --- snakePipes/shared/rules/envs/shared.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/snakePipes/shared/rules/envs/shared.yaml b/snakePipes/shared/rules/envs/shared.yaml index f4f0af652..d5034726b 100755 --- a/snakePipes/shared/rules/envs/shared.yaml +++ b/snakePipes/shared/rules/envs/shared.yaml @@ -15,6 +15,6 @@ dependencies: - multiqc = 1.23 - fastp = 0.23.4 - umi_tools = 1.1.4 - - bioconda::fq = 0.13.0 + - bioconda::fq = 0.12.0 - pybigwig = 0.3.22 From f635db7aa4ab2e90156056216bb1f7dc02d4bcbd Mon Sep 17 00:00:00 2001 From: WardDeb Date: Tue, 22 Oct 2024 14:41:59 +0200 Subject: [PATCH 34/35] bioconda > conda-forge --- snakePipes/shared/rules/envs/shared.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/snakePipes/shared/rules/envs/shared.yaml b/snakePipes/shared/rules/envs/shared.yaml index d5034726b..8e4e90325 100755 --- a/snakePipes/shared/rules/envs/shared.yaml +++ b/snakePipes/shared/rules/envs/shared.yaml @@ -1,7 +1,7 @@ name: snakepipes_shared_environment_2.0 channels: - - conda-forge - bioconda + - conda-forge dependencies: - python = 3.10.13 - deeptools = 3.5.4 @@ -15,6 +15,6 @@ dependencies: - multiqc = 1.23 - fastp = 0.23.4 - umi_tools = 1.1.4 - - bioconda::fq = 0.12.0 + - fq = 0.12.0 - pybigwig = 0.3.22 From 1a0d33d40dfa391b26b27b3aa83c93cb2a6bc8d9 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Tue, 22 Oct 2024 14:49:59 +0200 Subject: [PATCH 35/35] separate env for fq lint --- .github/workflows/linux.yml | 3 ++- .github/workflows/osx.yml | 3 ++- snakePipes/common_functions.py | 4 +++- snakePipes/shared/rules/FASTQ.snakefile | 4 ++-- snakePipes/shared/rules/envs/fqlint.yaml | 4 ++++ snakePipes/shared/rules/envs/shared.yaml | 3 +-- 6 files changed, 14 insertions(+), 7 deletions(-) create mode 100644 snakePipes/shared/rules/envs/fqlint.yaml diff --git a/.github/workflows/linux.yml b/.github/workflows/linux.yml index b9723025f..492e4f29c 100644 --- a/.github/workflows/linux.yml +++ b/.github/workflows/linux.yml @@ -100,7 +100,8 @@ jobs: 'CONDA_PREPROCESSING_ENV', 'CONDA_NONCODING_RNASEQ_ENV', 'CONDA_SAMBAMBA_ENV', - 'CONDA_pysam_ENV' + 'CONDA_pysam_ENV', + 'CONDA_FQLINT_ENV' ] runs-on: ubuntu-latest steps: diff --git a/.github/workflows/osx.yml b/.github/workflows/osx.yml index 667c9e168..944e73ab0 100644 --- a/.github/workflows/osx.yml +++ b/.github/workflows/osx.yml @@ -31,7 +31,8 @@ jobs: 'CONDA_PREPROCESSING_ENV', 'CONDA_NONCODING_RNASEQ_ENV', 'CONDA_SAMBAMBA_ENV', - 'CONDA_pysam_ENV' + 'CONDA_pysam_ENV', + 'CONDA_FQLINT_ENV' ] runs-on: macos-latest steps: diff --git a/snakePipes/common_functions.py b/snakePipes/common_functions.py index 1bae3bfb6..059a3e366 100644 --- a/snakePipes/common_functions.py +++ b/snakePipes/common_functions.py @@ -42,7 +42,9 @@ def set_env_yamls(): 'CONDA_NONCODING_RNASEQ_ENV': 'envs/noncoding.yaml', 'CONDA_SAMBAMBA_ENV': 'envs/sambamba.yaml', 'CONDA_pysam_ENV': 'envs/pysam.yaml', - 'CONDA_SEACR_ENV': 'envs/chip_seacr.yaml'} + 'CONDA_SEACR_ENV': 'envs/chip_seacr.yaml', + 'CONDA_FQLINT_ENV': 'envs/fqlint.yaml' + } def merge_dicts(x, y): diff --git a/snakePipes/shared/rules/FASTQ.snakefile b/snakePipes/shared/rules/FASTQ.snakefile index b40904845..7802d43fa 100755 --- a/snakePipes/shared/rules/FASTQ.snakefile +++ b/snakePipes/shared/rules/FASTQ.snakefile @@ -5,7 +5,7 @@ if pairedEnd or pipeline=="scrnaseq": r2 = indir+"/{sample}"+reads[1]+ext output: temp("originalFASTQ/{sample}.valid") - conda: CONDA_SHARED_ENV + conda: CONDA_FQLINT_ENV shell:""" fq lint {input.r1} {input.r2} touch {output} @@ -16,7 +16,7 @@ else: r1 = indir+"/{sample}"+reads[0]+ext output: temp("originalFASTQ/{sample}.valid") - conda: CONDA_SHARED_ENV + conda: CONDA_FQLINT_ENV shell:""" fq lint {input.r1} touch {output} diff --git a/snakePipes/shared/rules/envs/fqlint.yaml b/snakePipes/shared/rules/envs/fqlint.yaml new file mode 100644 index 000000000..e3128b9a0 --- /dev/null +++ b/snakePipes/shared/rules/envs/fqlint.yaml @@ -0,0 +1,4 @@ +channels: + - bioconda +dependencies: + - fq = 0.12.0 \ No newline at end of file diff --git a/snakePipes/shared/rules/envs/shared.yaml b/snakePipes/shared/rules/envs/shared.yaml index 8e4e90325..d2985672d 100755 --- a/snakePipes/shared/rules/envs/shared.yaml +++ b/snakePipes/shared/rules/envs/shared.yaml @@ -1,7 +1,7 @@ name: snakepipes_shared_environment_2.0 channels: - - bioconda - conda-forge + - bioconda dependencies: - python = 3.10.13 - deeptools = 3.5.4 @@ -15,6 +15,5 @@ dependencies: - multiqc = 1.23 - fastp = 0.23.4 - umi_tools = 1.1.4 - - fq = 0.12.0 - pybigwig = 0.3.22