Question: How to use Snakemake with tools which don't have clearly defined output options for files?
0
gravatar for Artem Kiselev
2.0 years ago by
Russian Federation
Artem Kiselev30 wrote:

Hi, I would like to use Snakemake in my variant annotation pipeline. But Annovar don't have clearly defined file output option (I can assign only output folder and annovar going to attach to filename: "multianno.hg19), I can't describe final annovar output in "rule all", since it differs from the output parameters in rule for annovar tool. Help, please solve this problem. Thank you!

ADD COMMENTlink modified 2.0 years ago by WouterDeCoster44k • written 2.0 years ago by Artem Kiselev30
1
gravatar for WouterDeCoster
2.0 years ago by
Belgium
WouterDeCoster44k wrote:

You specify output files that are created, and use a params value for your shell code.

Example below for mosdepth:
I specify that mosdepth/{sample}.mosdepth.global.dist.txt will be created, but as output value for my shell command I use mosdepth/{params.prefix}, which takes the sample name.
Mosdepth will create mosdepth/{sample}.mosdepth.global.dist.txt

rule mosdepth_get:
    input:
        bam = "alignment/{sample}.bam",
        bai = "alignment/{sample}.bam.bai"
    output:
        protected("mosdepth/{sample}.mosdepth.global.dist.txt"),
        protected("mosdepth/{sample}.regions.bed.gz"),
    params:
        windowsize = 500,
        prefix = "{sample}",
    log:
        "logs/{aligner}/mosdepth/mosdepth_{sample}.log"
    shell:
        "mosdepth -n --by {params.windowsize} mosdepth/{params.prefix} {input.bam} 2> {log}"
ADD COMMENTlink written 2.0 years ago by WouterDeCoster44k
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