rnaseq_workflow/Snakefile at master · ianbed/rnaseq_workflow · GitHub

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import pandas as pd
from snakemake.utils import validate, min_version
##### set minimum snakemake version #####
min_version("5.4.4")


##### load config and sample sheets #####

configfile: "src/config.yaml"
validate(config, schema="schemas/config.schema.yaml")

units = pd.read_table(config["units"]).set_index("sample", drop=False)
validate(units, schema="schemas/units.schema.yaml")

contrasts = pd.read_table(config["contrasts"]).set_index("contrast", drop=False)
validate(contrasts, schema="schemas/contrasts.schema.yaml")

##### target rules #####

rule all:
    input:
        # test
        # expand("trimmed/{units.sample}-{units.unit}.1.fastq.gz", units=units.itertuples()),
        # expand("trimmed/{units.sample}-{units.unit}.2.fastq.gz", units=units.itertuples()),
        # expand("trimmed/{units.sample}-{units.unit}.qc.txt", units=units.itertuples()),
        # symlink
        # expand("raw_reads/{units.sample}-{units.unit}.fastq.gz", units=units.itertuples()), #SE
        # expand("raw_reads/{units.sample}_{units.unit}_R1.fastq.gz", units=units.itertuples()),
        # expand("raw_reads/{units.sample}_{units.unit}_R2.fastq.gz", units=units.itertuples()),
        # fastqc
        # expand("qc/fastqc/{units.sample}-{units.unit}_fastqc.html", units=units.itertuples()), #SE
        # expand("qc/fastqc/{units.sample}_{units.unit}_R1_fastqc.html", units=units.itertuples()),
        # expand("qc/fastqc/{units.sample}_{units.unit}_R2_fastqc.html", units=units.itertuples()),
        # Trim_Galore
        # expand("trimmed_data/{units.sample}-{units.unit}_trimmed.fq.gz", units=units.itertuples()), #SE
        # expand("trimmed_data/{units.sample}_{units.unit}_R1_val_1.fq.gz", units=units.itertuples()),
        # expand("trimmed_data/{units.sample}_{units.unit}_R2_val_2.fq.gz", units=units.itertuples()),
        # STAR alignment
        # expand("analysis/star/{units.sample}_{units.unit}.Aligned.out.bam", units=units.itertuples()),
        # expand("analysis/star/{units.sample}_{units.unit}.Log.out", units=units.itertuples()),
        # sort_index_bam
        # expand("analysis/star/{units.sample}_{units.unit}.sorted.bam", units=units.itertuples()),
        # expand("analysis/star/{units.sample}_{units.unit}.sorted.bam.bai", units=units.itertuples()),
        # count_matrix
        # "deliverables/counts.tsv",
        # "deliverables/UniquelyMappingRates.txt",
        # "deliverables/UniquelyMappingReads.txt",
        # "deliverables/starMatrix.txt",
        #multiqc
        # "qc/multiqc_report.html",
        # edger
        "deliverables/edgeR_longReport.html",


##### load rules #####
include: "rules/align.smk"
include: "rules/common.smk"
include: "rules/count_matrix.smk"
include: "rules/edger.smk"
include: "rules/fastqc.smk"
include: "rules/get_mapping_rates.smk"
include: "rules/multiqc.smk"
include: "rules/sort_index_bam.smk"
include: "rules/symlink.smk"
include: "rules/trim.smk"