How to input list into GenomicsDBImport with snakemake?

Question

[ema]

Hello!

I'm currently writing a pipeline with snakemake for exome data. During joint variant calling I need to use GATK's GenomicsDBImport, although I'm unsure how to input all the samples at once. Here's the simplified version of the rule I'm using:

rule GenomicsDBImport:
    input:
        gvcf = expand("variant_call/{sample}_raw_variants.g.vcf", sample=SAMPLE),
        ref = REF
    output:
        dir = "GDBI_database"
    shell:
        """
        ({GATK} GenomicsDBImport  -R {input.ref} -V {input.gvcf} --genomicsdb-workspace-path {output.dir}) 2> {log}
        """

From my understanding, the expand function gives me a list of all the sample names as strings. My question is: can the '-V' argument take a list as input? There's also the option to use a snakemake wrapper, but I'm unfamiliar with that method.

Thanks in advance!

[Ram]

You'd need to take the map-file route, I think. The wrapper does a better job using this line:

gvcfs = list(map("--variant {}".format, snakemake.input.gvcfs))

You could add that code and try if this works:

input:
        gvcf = list(map("--variant {}".format, expand("variant_call/{sample}_raw_variants.g.vcf", sample=SAMPLE))),
        ref = REF

The above code is just theoretical, completely untested.