Samples mismatch issue while running nextflow module

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1

I am using Sarek pipeline of nf-core, on which I build a module called TMB where I am taking two inputs - SnpEff annotated vcf file and HS metrics file produced as as from two different modules.
When the TMB module is running, the vcf and hs metrics are not belonging to same sample. This module is executed as sample-wise.

Here is how I am calling the TMB module from my workflow

  bam_from_markduplicates = BAM_MARKDUPLICATES.out.bam_markdup
 
    HS_Metrics(BAM_MARKDUPLICATES.out.bam_markdup,TI_BI)

    // HS_Metrics.out.HS_Metrics.view()
//     VCF_ANNOTATE_ALL.out.vcf_ann.view()
 
    if (params.tools.split(',').contains('mutect2')) {
    TMB_merged_inputs = HS_Metrics.out.HS_Metrics.join(VCF_ANNOTATE_ALL.out.vcf_ann, by: ['sample'])
    TMB_merged_inputs.view { it }
        TMB(
            TMB_merged_inputs,
            fasta,Exome_file,cds)

Output from HS metrics

  tuple val(meta), path ("${prefix}_HSmetrics.csv"), emit: HS_Metrics

TMB module :


    label 'process_medium'

    input:
    tuple val(meta),path(HS_Metrics),val(meta),path(vcf),path(vcf_index)
    path(fasta)
    path(Exome_file)

    output:
    tuple val(meta),path("*.csv"), emit: tmb_metrics

    script:
    """
	cp ${projectDir}/bin/vcf2maf.pl .
	Rscript ${projectDir}/bin/tmb.R  --vcf_file $vcf --ref_fasta $fasta --outpath ./ --cds_file ${projectDir}/resources/cds.bed --exome_file $Exome_file --coverages 40_100_250 --hsmetrics $HS_Metrics --sample_id ${meta.id}
"""
}

However, when the module is executed, I am getting 2 files from 2 different samples.

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image1573×358 78.8 KB

Can you please help me understand what can be going wrong.

2

You are joining by a specific field in your meta map. I don’t think this feature has been implemented yet.