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snakemake output directory

I am new to snakemake. I have a simple quesiton and I can not do the fastqc output into a directory

rule run_fastqc:
    input:
        "data/ERR127302_1_subset.fastq.gz"
    output:
        directory("result/")
    shell:
        "fastqc {input} -o {output} "

I try the command:

snakemake -j 1 -n

The output is:

Building DAG of jobs...
Nothing to be done.

is there any advices ? Thanks.

snakemake ngs
• 6,612 views • link
updated by 进 • 进 • written by Peter Chung Peter Chung

2 answers

I can successfully output the result to the result directory.

rule run_fastqc:
    input:
        "data/ERR127302_1_subset.fastq.gz"
    output:
        "result/{sample}_fastqc.html",
        "result/{sample}_fastqc.zip"
    params:
        dir="result"
    shell:
        "fastqc {input} -o {params.dir}"

The html file and the zip will be in the result directory

• 0 views • link
written by Peter Chung Peter Chung

it is right answer

• 0 views • link
written by 进 • 进

Nothing to be done suggests the output, i.e. directory results, exists and is newer than the input so no need to rerun the jobs.

• 0 views • link
written by dariober dariober

I want the fastqc output file, the html file and the zip file output to result directory but it output nothing.

I tried to change the output in the Snakefile like below:

output:
    expand("result/{sample}_fastqc.html",sample=SAMPLES),
    expand("result/{sample}_fastqc.zip",sample=SAMPLES)

but it still outputs to the data directory, do you know why

• 0 views • link
written by Peter Chung Peter Chung

Did you define rule all?

• 0 views • link
written by cpad0112 cpad0112

no, I didn't. what should I input in rule all 

rule all:
    input:
        expand("result/{sample}_fastqc.html",sample=SAMPLES),
        expand("result/{sample}_fastqc.zip",sample=SAMPLES)

it stills output at the data directory

• 0 views • link
written by Peter Chung Peter Chung

Try this as shell command: fastqc {input} -q -f fastq -o result/

• 0 views • link
written by cpad0112 cpad0112

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