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author
mykle hoban
committed
various updates, including adding braces to if statements
1 parent f4ae4fb commit 5ba8d95

2 files changed

Lines changed: 89 additions & 83 deletions

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‎eDNAFlow.nf‎

Lines changed: 89 additions & 82 deletions
Original file line numberDiff line numberDiff line change
@@ -89,10 +89,8 @@ def helpMessage() {
8989
9090
Choice of USEARCH32 vs USEARCH64
9191
--mode [str] Default is '${params.mode}'; for running with 64 version the mode has to be set to --mode 'usearch64'
92-
and below --search64 option has to be specified as well; can set to --mode 'vsearch' (only if --skipDemux is also chosen)
93-
below --vsearch option has to be specified as well
92+
and below --search64 option has to be specified as well; can set to --mode 'vsearch'
9493
--usearch64 [dir] Full path to where usearch64 bit version is stored locally
95-
--vsearch [dir] Full path to where vsearch bit version is stored locally
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9795
LULU
9896
--lulu [file] An R script to run post-clustering curation with default settings of LULU;
@@ -134,7 +132,6 @@ qcov = params.qcov
134132
lulu = file(params.lulu)
135133
mode = params.mode
136134
usearch64 = params.usearch64
137-
vsearch = params.vsearch
138135
minMatch_lulu = params.minMatch_lulu
139136

140137
// Setting up channels & inputs for taxonomy assignment step
@@ -322,20 +319,24 @@ process '03_Length_filtered' {
322319

323320
script:
324321
if (params.illumina_demultiplexed)
325-
"""
326-
cat "${fastq_files}" > "${sample_id}_QF_Dmux.fastq"
327-
obiannotate -S sample:'"_".join(sequence.getDefinition().strip().split("_")[1:])' "${sample_id}_QF_Dmux.fastq" > "${sample_id}_labelled.fastq"
328-
if ${params.remove_ambiguous_tags}; then
329-
obigrep -l $minLen "${sample_id}_labelled.fastq" | obigrep -v -D '1:N:0:.*[NBDHVKYSWRM].*_' > "${sample_id}_QF_Dmux_minLF.fastq"
330-
else
331-
obigrep -l $minLen "${sample_id}_labelled.fastq" > ${sample_id}_QF_Dmux_minLF.fastq
332-
fi
333-
"""
322+
{
323+
"""
324+
cat "${fastq_files}" > "${sample_id}_QF_Dmux.fastq"
325+
obiannotate -S sample:'"_".join(sequence.getDefinition().strip().split("_")[1:])' "${sample_id}_QF_Dmux.fastq" > "${sample_id}_labelled.fastq"
326+
if ${params.remove_ambiguous_tags}; then
327+
obigrep -l $minLen "${sample_id}_labelled.fastq" | obigrep -v -D '1:N:0:.*[NBDHVKYSWRM].*_' > "${sample_id}_QF_Dmux_minLF.fastq"
328+
else
329+
obigrep -l $minLen "${sample_id}_labelled.fastq" > ${sample_id}_QF_Dmux_minLF.fastq
330+
fi
331+
"""
332+
}
334333
else
335-
"""
336-
cat ${fastq_files} > "${sample_id}_QF_Dmux.fastq"
337-
obigrep -l $minLen -p 'forward_tag is not None and reverse_tag is not None' "${sample_id}_QF_Dmux.fastq" > "${sample_id}_QF_Dmux_minLF.fastq"
338-
"""
334+
{
335+
"""
336+
cat ${fastq_files} > "${sample_id}_QF_Dmux.fastq"
337+
obigrep -l $minLen -p 'forward_tag is not None and reverse_tag is not None' "${sample_id}_QF_Dmux.fastq" > "${sample_id}_QF_Dmux_minLF.fastq"
338+
"""
339+
}
339340
}
340341

341342

@@ -390,7 +391,7 @@ process '05_relabel_Cat_vsearch' {
390391
do
391392
label=\$(echo \$files | cut -d '/' -f 3 | cut -d '.' -f 1)
392393
# $usearch64 -fastx_relabel \$files -prefix \${label}. -fastqout \${label}.relabeled.fastq
393-
vsearch --fastx_filter \$files --relabel \${label}. --fastqout \${label}.relabeled.fastq
394+
vsearch --threads ${task.cpus} --fastx_filter \$files --relabel \${label}. --fastqout \${label}.relabeled.fastq
394395
done
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for files in *.relabeled.fastq
@@ -407,7 +408,7 @@ process '05_relabel_Cat_vsearch' {
407408
# $usearch64 -fastx_get_sample_names *_relabeled4Usearch.fastq -output sample.txt
408409
409410
# $usearch64 -fastq_filter *_relabeled4Usearch.fastq -fastaout ${sample_id}.fasta
410-
vsearch --fastx_filter *_relabeled4Usearch.fastq --fastaout ${sample_id}.fasta
411+
vsearch --threads ${task.cpus} --fastx_filter *_relabeled4Usearch.fastq --fastaout ${sample_id}.fasta
411412
412413
awk '/^>/ {print(\$0)}; /^[^>]/ {print(toupper(\$0))}' *.fasta > ${sample_id}_upper.fasta
413414
"""
@@ -428,53 +429,55 @@ process '05_relabel_Cat_usearch' {
428429

429430

430431
script:
431-
if(mode == 'usearch32')
432-
"""
433-
for files in ${fastqs}
434-
do
435-
label=\$(echo \$files | cut -d '/' -f 3 | cut -d '.' -f 1)
436-
usearch -fastx_relabel \$files -prefix \${label}. -fastqout \${label}.relabeled.fastq
437-
done
438-
439-
for files in *.relabeled.fastq
440-
do
441-
name=\$(echo \$files | cut -d '/' -f '2' | cut -d '.' -f 1)
442-
echo \${name} >> CountOfSeq.txt
443-
grep "^@\${name}" \$files | wc -l >> CountOfSeq.txt
444-
done
445-
446-
cat *.relabeled.fastq > "${sample_id}_QF_Dmux_minLF_relabeled4Usearch.fastq"
447-
448-
usearch -fastx_get_sample_names *_relabeled4Usearch.fastq -output sample.txt
449-
450-
usearch -fastq_filter *_relabeled4Usearch.fastq -fastaout ${sample_id}.fasta
451-
452-
awk '/^>/ {print(\$0)}; /^[^>]/ {print(toupper(\$0))}' *.fasta > ${sample_id}_upper.fasta
453-
454-
"""
455-
else if(mode == 'usearch64')
456-
"""
457-
for files in ${fastqs}
458-
do
459-
label=\$(echo \$files | cut -d '/' -f 3 | cut -d '.' -f 1)
460-
$usearch64 -fastx_relabel \$files -prefix \${label}. -fastqout \${label}.relabeled.fastq
461-
done
432+
if (mode == 'usearch32') {
433+
"""
434+
for files in ${fastqs}
435+
do
436+
label=\$(echo \$files | cut -d '/' -f 3 | cut -d '.' -f 1)
437+
usearch -fastx_relabel \$files -prefix \${label}. -fastqout \${label}.relabeled.fastq
438+
done
439+
440+
for files in *.relabeled.fastq
441+
do
442+
name=\$(echo \$files | cut -d '/' -f '2' | cut -d '.' -f 1)
443+
echo \${name} >> CountOfSeq.txt
444+
grep "^@\${name}" \$files | wc -l >> CountOfSeq.txt
445+
done
462446
463-
for files in *.relabeled.fastq
464-
do
465-
name=\$(echo \$files | cut -d '/' -f '2' | cut -d '.' -f 1)
466-
echo \${name} >> CountOfSeq.txt
467-
grep "^@\${name}" \$files | wc -l >> CountOfSeq.txt
468-
done
469-
470-
cat *.relabeled.fastq > "${sample_id}_QF_Dmux_minLF_relabeled4Usearch.fastq"
471-
472-
$usearch64 -fastx_get_sample_names *_relabeled4Usearch.fastq -output sample.txt
473-
474-
$usearch64 -fastq_filter *_relabeled4Usearch.fastq -fastaout ${sample_id}.fasta
447+
cat *.relabeled.fastq > "${sample_id}_QF_Dmux_minLF_relabeled4Usearch.fastq"
448+
449+
usearch -fastx_get_sample_names *_relabeled4Usearch.fastq -output sample.txt
450+
451+
usearch -fastq_filter *_relabeled4Usearch.fastq -fastaout ${sample_id}.fasta
452+
453+
awk '/^>/ {print(\$0)}; /^[^>]/ {print(toupper(\$0))}' *.fasta > ${sample_id}_upper.fasta
454+
455+
"""
456+
}
457+
else if (mode == 'usearch64') {
458+
"""
459+
for files in ${fastqs}
460+
do
461+
label=\$(echo \$files | cut -d '/' -f 3 | cut -d '.' -f 1)
462+
$usearch64 -fastx_relabel \$files -prefix \${label}. -fastqout \${label}.relabeled.fastq
463+
done
475464
476-
awk '/^>/ {print(\$0)}; /^[^>]/ {print(toupper(\$0))}' *.fasta > ${sample_id}_upper.fasta
477-
"""
465+
for files in *.relabeled.fastq
466+
do
467+
name=\$(echo \$files | cut -d '/' -f '2' | cut -d '.' -f 1)
468+
echo \${name} >> CountOfSeq.txt
469+
grep "^@\${name}" \$files | wc -l >> CountOfSeq.txt
470+
done
471+
472+
cat *.relabeled.fastq > "${sample_id}_QF_Dmux_minLF_relabeled4Usearch.fastq"
473+
474+
$usearch64 -fastx_get_sample_names *_relabeled4Usearch.fastq -output sample.txt
475+
476+
$usearch64 -fastq_filter *_relabeled4Usearch.fastq -fastaout ${sample_id}.fasta
477+
478+
awk '/^>/ {print(\$0)}; /^[^>]/ {print(toupper(\$0))}' *.fasta > ${sample_id}_upper.fasta
479+
"""
480+
}
478481
}
479482

480483
ch = mode == 'vsearch' ? relabel_ch_vsearch : relabel_ch_usearch
@@ -503,12 +506,12 @@ process '06_Uniques_ZOTUs_vsearch' {
503506

504507
script:
505508
"""
506-
vsearch --derep_fulllength ${upper_fasta} --sizeout --output "${sample_id}_Unq.fasta"
509+
vsearch --threads ${task.cpus} --derep_fulllength ${upper_fasta} --sizeout --output "${sample_id}_Unq.fasta"
507510
508-
vsearch --cluster_unoise "${sample_id}_Unq.fasta" --centroids "${sample_id}_centroids.fasta" --minsize $minsize
509-
vsearch --uchime3_denovo "${sample_id}_centroids.fasta" --nonchimeras "${sample_id}_zotus.fasta" --relabel zotu
511+
vsearch --threads ${task.cpus} --cluster_unoise "${sample_id}_Unq.fasta" --centroids "${sample_id}_centroids.fasta" --minsize $minsize
512+
vsearch --threads ${task.cpus} --uchime3_denovo "${sample_id}_centroids.fasta" --nonchimeras "${sample_id}_zotus.fasta" --relabel zotu
510513
511-
vsearch --usearch_global ${upper_fasta} --db "${sample_id}_zotus.fasta" --id 0.97 --otutabout zotuTable.txt
514+
vsearch --threads ${task.cpus} --usearch_global ${upper_fasta} --db "${sample_id}_zotus.fasta" --id 0.97 --otutabout zotuTable.txt
512515
"""
513516
}
514517

@@ -528,21 +531,25 @@ process '06_Uniques_ZOTUs_usearch' {
528531

529532
script:
530533
if(mode == 'usearch32')
531-
"""
532-
usearch -fastx_uniques ${upper_fasta} -sizeout -fastaout "${sample_id}_Unq.fasta"
533-
534-
usearch -unoise3 "${sample_id}_Unq.fasta" -zotus "${sample_id}_zotus.fasta" -tabbedout "${sample_id}_Unq_unoise3.txt" -minsize $minsize
535-
536-
usearch -otutab ${upper_fasta} -zotus ${sample_id}_zotus.fasta -otutabout zotuTable.txt -mapout zmap.txt
537-
"""
534+
{
535+
"""
536+
usearch -fastx_uniques ${upper_fasta} -sizeout -fastaout "${sample_id}_Unq.fasta"
537+
538+
usearch -unoise3 "${sample_id}_Unq.fasta" -zotus "${sample_id}_zotus.fasta" -tabbedout "${sample_id}_Unq_unoise3.txt" -minsize $minsize
539+
540+
usearch -otutab ${upper_fasta} -zotus ${sample_id}_zotus.fasta -otutabout zotuTable.txt -mapout zmap.txt
541+
"""
542+
}
538543
else if(mode == 'usearch64')
539-
"""
540-
$usearch64 -fastx_uniques ${upper_fasta} -sizeout -fastaout "${sample_id}_Unq.fasta"
541-
542-
$usearch64 -unoise3 "${sample_id}_Unq.fasta" -zotus "${sample_id}_zotus.fasta" -tabbedout "${sample_id}_Unq_unoise3.txt" -minsize $minsize
543-
544-
$usearch64 -otutab ${upper_fasta} -zotus ${sample_id}_zotus.fasta -otutabout zotuTable.txt -mapout zmap.txt
545-
"""
544+
{
545+
"""
546+
$usearch64 -fastx_uniques ${upper_fasta} -sizeout -fastaout "${sample_id}_Unq.fasta"
547+
548+
$usearch64 -unoise3 "${sample_id}_Unq.fasta" -zotus "${sample_id}_zotus.fasta" -tabbedout "${sample_id}_Unq_unoise3.txt" -minsize $minsize
549+
550+
$usearch64 -otutab ${upper_fasta} -zotus ${sample_id}_zotus.fasta -otutabout zotuTable.txt -mapout zmap.txt
551+
"""
552+
}
546553
}
547554

548555
zotu_ch = mode == 'vsearch' ? zotu_ch_vsearch : zotu_ch_usearch

‎nextflow.config‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -37,7 +37,6 @@ params {
3737
lulu = "lulu.R"
3838
mode = "usearch32"
3939
usearch64 = ""
40-
vsearch = ""
4140
blast_db = ""
4241
custom_db = ""
4342
blast_task = "blastn"

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