Snakemake Fastqc: "Multiple run or shell keywords in rule run_fastqc."

Question

I am trying to check the quality of RNA-Seq data from Illumina using fastqc in snakemake in a conda environment. I get the error "Multiple run or shell keywords in rule run_fastqc".

Snakefile:

rule run_fastqc:
    input:
        "/[RNA fastq file path]/well01_S001_L001_R1_001.fastq.gz"
    output:
        "./[out path]/well01_S001_L001_R1_001.fastqc.html",
        "./[out path]/well01_S001_L001_R1_001.fastqc.zip"
    wrapper:
        "0.79.0/bio/fastqc"
    shell:
        "fastqc {input} --outdir=./[out path]/"

I've also tried:

...
    shell:
        "fastqc {input} -o ./[out path]/"
...
    shell:
        "fastqc -o ./[out path]/ {input}"
...
    shell:
        "fastqc {input}"
        "fastqc -o ./[out path]/"
...
    shell:
        "fastqc {input} > -o ./[out path]/"

Code:

snakemake --cores 1 well01_S001_L001_R1_001.fastqc.html well01_S001_L001_R1_001.fastqc.zip

Output:

SyntaxError in line 9 of /[path to Snakefile]/Snakefile:
Multiple run or shell keywords in rule run_fastqc. (Snakefile, line 9)

When I run fastqc alone (not in snakemake), it works and I get the two output files. How can I get snakemake to work?

Thank you for your time and help!

Answer 1

From a quick look at the manual, it looks like you are supposed to use just the wrapper, not combine the wrapper with a shell. Can you show me an example of such combined usage?

The error seems to suggest that the wrapper already has a shell directive that you shell conflicts with.