why my process only open once?

[huangl07]

Hi, I have already generate a code like this:

process vcffilter{
    publishDir "${params.outdir}/01.filter", pattern:"*"
    queue "DNA"
    cpus 8
    executor "slurm"
    memory "30G"
        cache 'lenient'

    input:
        file vcf from vcf_file
    output:
        file "pop.filtered.vcf.gz" into filter_vcf1,filter_vcf2
        file "pop.filtered.vcf.gz.tbi" into vcf_index
    script:
    """
        bcftools filter --threads 8  -O z -i "F_Missing <=${params.miss} && MAF > ${params.maf} && FORMAT/DP < ${params.dep}" ${vcf}  > pop.filtered.vcf.gz
        tabix pop.filtered.vcf.gz
    """
}


process group_preparie{
    publishDir "${params.outdir}/02.group", pattern:"*"
    queue "DNA"
    cpus 8
    executor "slurm"
    memory "30G"
        cache 'lenient'

    input:
        file group from group_file
    output:
        file "group.list" into  grouplist1,grouplist2
    script:
    """
        perl ${baseDir}/bin/group.pl -i ${group} -o ./
    """
}
grouplist2.splitCsv(header:false,sep:'\t').map(it->it).set{groups}
process tajimaD1{
    publishDir "${params.outdir}/03.tajimaD", pattern:"*"
    queue "DNA"
    cpus 8
    executor "slurm"
    memory "30G"
    cache 'lenient'
    input:
        file vcf from filter_vcf2
        tuple gid,gfile from groups
    output:
        file "*.Tajima.D" 
    script:
    """
       vcftools --gzvcf ${vcf} --remove-indels --TajimaD ${params.win} --keep ${gfile[0]} --out ${gid[1]}
    """
}

the group_prepaired and vcffilter is ok but the tajimaD is ambiguous

the grouplist2 file is like this

Cn^I/mnt/ilustre/users/dna/Development/POP/SG/2022-5-19/work/bc/380f7a03436a5596b4102aa89d6dd1/Cn.txt$
DH2^I/mnt/ilustre/users/dna/Development/POP/SG/2022-5-19/work/bc/380f7a03436a5596b4102aa89d6dd1/DH2.txt$
DH^I/mnt/ilustre/users/dna/Development/POP/SG/2022-5-19/work/bc/380f7a03436a5596b4102aa89d6dd1/DH.txt$
DSH^I/mnt/ilustre/users/dna/Development/POP/SG/2022-5-19/work/bc/380f7a03436a5596b4102aa89d6dd1/DSH.txt$
HD^I/mnt/ilustre/users/dna/Development/POP/SG/2022-5-19/work/bc/380f7a03436a5596b4102aa89d6dd1/HD.txt$
JD2^I/mnt/ilustre/users/dna/Development/POP/SG/2022-5-19/work/bc/380f7a03436a5596b4102aa89d6dd1/JD2.txt$
JD^I/mnt/ilustre/users/dna/Development/POP/SG/2022-5-19/work/bc/380f7a03436a5596b4102aa89d6dd1/JD.txt$
PY^I/mnt/ilustre/users/dna/Development/POP/SG/2022-5-19/work/bc/380f7a03436a5596b4102aa89d6dd1/PY.txt$
TZ^I/mnt/ilustre/users/dna/Development/POP/SG/2022-5-19/work/bc/380f7a03436a5596b4102aa89d6dd1/TZ.txt$

but when I run the code ,the process tajimaD only generate one task ?

why?

thankyou

[bentsherman]

Hi @huangl07 , how many vcf files are produced by the vcffilter process? If there is only one, then the tajimaD1 process will run only once. If you need to reuse the same vcf file for each group then you should change the vcf input to:

each file(vcf) from filter_vcf2

Or, make the vcf_file channel a value channel so that the downstream filter_vcf2 channel can be reused many times.