CODEWITHSUNDEEP
pythonbioinformaticssnakemakevcf-variant-call-formatbcftools
Kelly Sovacool
Kelly Sovacool

Reputation: 93

Best way to run same rule twice with different params

I'm using bcftools consensus to extract haplotypes from a vcf file. Given the input files:

A.sorted.bam
B.sorted.bam

The following output files are created:

A.hap1.fna
A.hap2.fna
B.hap1.fna
B.hap2.fna

I currently have two rules to do this. They differ only by the numbers 1 and 2 in the output files and shell command. Code:

rule consensus1:
    input:
        vcf="variants/phased.vcf.gz",
        tbi="variants/phased.vcf.gz.tbi",
        bam="alignments/{sample}.sorted.bam"
    output:
        "haplotypes/{sample}.hap1.fna"
    params:
        sample="{sample}"
    shell:
        "bcftools consensus -i -s {params.sample} -H 1 -f {reference_file} {input.vcf} > {output}"

rule consensus2:
    input:
        vcf="variants/phased.vcf.gz",
        tbi="variants/phased.vcf.gz.tbi",
        bam="alignments/{sample}.sorted.bam"
    output:
        "haplotypes/{sample}.hap2.fna"
    params:
        sample="{sample}"
    shell:
        "bcftools consensus -i -s {params.sample} -H 2 -f {reference_file} {input.vcf} > {output}"

While this code works, it seems that there should be a better, more pythonic way to do this using only one rule. Is it possible to collapse this into one rule, or is my current method the best way?

Upvotes: 1

Views: 1370

Answers (1)

Manavalan Gajapathy
Manavalan Gajapathy

Reputation: 4089

Use wildcards for haplotypes 1 and 2 in rule all. See here to learn more about adding targets via rule all

reference_file = "ref.txt"

rule all:
    input:
        expand("haplotypes/{sample}.hap{hap_no}.fna",
                   sample=["A", "B"], hap_no=["1", "2"])

rule consensus1:
    input:
        vcf="variants/phased.vcf.gz",
        tbi="variants/phased.vcf.gz.tbi",
        bam="alignments/{sample}.sorted.bam"
    output:
        "haplotypes/{sample}.hap{hap_no}.fna"
    params:
        sample="{sample}",
        hap_no="{hap_no}"
    shell:
        "bcftools consensus -i -s {params.sample} -H {params.hap_no} \
               -f {reference_file} {input.vcf} > {output}"

Upvotes: 2

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