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How to use a for loop to access inputs in snakemake?

I want to use the gatk MakeVcfSampleNameMap tool to generate a tab-delimited file that maps sample names to the corresponding VCF files in a Snakemake workflow. These vcfs are in a the directory input/

output - > (sample_name_map.txt)

input/vcf1.vcf.gz   control5-a
input/vcf2.vcf.gz   control5-c

MakeVcfSampleNameMap accepts a single --INPUT argument at a time, so I have to submit multiple VCF files to it in the form:

  • --INPUT {input.vcfs[0]}
  • --INPUT {input.vcfs[1]}, etc.

snakemake rule:

rule MakeVcfSampleNameMap:
    input:
        vcfs=["input/vcf1.vcf.gz", "input/vcf2.vcf.gz"],
    output:
        "sample_name_map.txt",
    shell:
        "gatk MakeVcfSampleNameMap \
        --INPUT {input.vcfs[0]} \
        --INPUT {input.vcfs[1]} \
        --OUTPUT {output}"

This becomes cumbersome when there are many input files. How can use a loop in the Snakemake rule to access all the VCF files?



source https://stackoverflow.com/questions/75700654/how-to-use-a-for-loop-to-access-inputs-in-snakemake

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