Snakemake: rename fastQC output in one rule

Question

I'm trying to combine these two rules together

rule fastqc:
    input:
        fastq = "{sample}.fastq.gz",
    output:
        zip1 = "{sample}_fastqc.zip",
        html = "{sample}_fastqc.html",
    threads:8
    shell:
        "fastqc -t {threads} {input.fastq}"

rule renamefastqc:
    input:
        zip1 = "{sample}_fastqc.zip",
        html = "{sample}_fastqc.html",
    output:
        zip1 = "{sample}__fastqc.zip",
        html = "{sample}__fastqc.html",
    shell:
        "mv {input.zip} {output.zip} && "
        "mv {input.html} {output.html} "

To look like this.

rule fastqc:
    input:
        fastq = "{sample}.fastq.gz"
    output:
        zip1 = "{sample}__fastqc.zip",
        html = "{sample}__fastqc.html"
    threads:8
    shell:
        "fastqc -t {threads} {input.fastq} && "
        "mv {outfile.zip} {output.zip1} && "
        "mv {outfile.html} {output.html}"

FastQC cannot specify file outputs and will always take a file ending in fastq.gz and create two files ending in _fastqc.zip and _fastqc.html. Normally I just write a rule that takes in those outputs and produces the one with two underscores (renamefastqc rule). But this means everytime I run the pipeline, snakemake sees that the outputs for the fastqc rule are gone and it wants to rebuild them. Therefore I'm trying to combine both rules into one step.

Manavalan Gajapathy Manavalan Gajapathy · Accepted Answer · 2018-06-15T20:13:12

You could use params to define files that are to be renamed.

rule all:
    input:
        "a123__fastqc.zip",

rule fastqc:
    input:
        fastq = "{sample}.fastq.gz",
    output:
        zip1 = "{sample}__fastqc.zip",
        html = "{sample}__fastqc.html",
    threads:8
    params:
        zip1 = lambda wildcards, output: output.zip1.replace('__', '_'),
        html = lambda wildcards, output: output.html.replace('__', '_')
    shell:
        """
        fastqc -t {threads} {input.fastq}
        mv {params.zip1} {output.zip1} \\
            && mv  {params.html} {output.html}
        """

Snakemake: rename fastQC output in one rule

1 Answers