Parallelise Output Of Input Function In Snakemake

Hello Snakemake community, I am having quite some troubles to define correctly a function in Snakemake and call it in the params section. The output of the function is a list and m

Solution 1:

What about this below? Note that your get_scontigs_names doesn't make use of wildcards.

import os, glob

defget_scontigs_names():
   scontigs = glob.glob(os.path.join("reference", "Supercontig*"))
   files = [os.path.basename(s) for s in scontigs]
   name = [i.split('_')[0] for i in files]
   return name

supercontigs= get_scontigs_names()

rule all:
    input:
        "updated/all_supercontigs.sorted.vcf.gz"

rule update_vcf:
    input:
        len="genome/genome_contigs_len_cumsum.txt",
        vcf="filtered/all.vcf.gz",
    output:
        upd= "updated/{supercontig}.updated.vcf.gz",
    shell:
        r"""
        python 3.7 scripts/update_genomic_reg.py -len {input.len} \
            -vcf {input.vcf} -scaf {wildcards.supercontig}
        """

rule list_updated: 
    input:
        expand("updated/{supercontig}.updated.vcf.gz", supercontig= supercontigs),
    output:
        "updated/all_supercontigs.sorted.vcf.gz",
    shell:
        r"""
        ls {input} > {output}
        """

Solution 2:

I have found the solution to my question inspired by @dariober.

rule all:
input:
    "updated/all_supercontigs.updated.list"import os, glob

defget_scontigs_names(wildcards):
    scontigs = glob.glob(os.path.join("reference", "Supercontig*"))
    files = [os.path.basename(s) for s in scontigs]
    name = [i.split('_')[0] for i in files]
    return name

rule update_vcf:
    input:
        len="genome/genome_contigs_len_cumsum.txt",
        vcf="filtered/all.vcf.gz"
    output:
        vcf="updated/all_{supercontig}.updated.vcf.gz"
    params:
        py3=config["modules"]["py3"],
        scaf=get_scontigs_names
    shell:
        """
        {params.py3} scripts/update_genomic_reg.py -len {input.len} -vcf 
        {input.vcf} -scaf {wildcards.supercontig}
        """


rule list_updated:
    input:
        expand("updated/all_{supercontig}.updated.vcf.gz", supercontig = 
        supercontigs)
    output:
        "updated/all_supercontigs.updated.list"
    shell:
        """
        ls {input} > {output}
        """