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Collect intervallist channel output and propagate to genotyping step #1872

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Collect intervallist channel output and propagate to genotyping step #1872

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e75687e
Collect intervallist channel output and propagate to genotyping step
percyfal Apr 24, 2025
47c0660
Move genomicsdbimport changes to nf-core modules
percyfal May 5, 2025
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7 changes: 4 additions & 3 deletions subworkflows/local/bam_joint_calling_germline_gatk/main.nf
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Expand Up @@ -46,9 +46,10 @@ workflow BAM_JOINT_CALLING_GERMLINE_GATK {

// Convert all sample vcfs into a genomicsdb workspace using genomicsdbimport
GATK4_GENOMICSDBIMPORT(gendb_input, false, false, false)

genotype_input = GATK4_GENOMICSDBIMPORT.out.genomicsdb.map{ meta, genomicsdb -> [ meta, genomicsdb, [], [], [] ] }

genotype_input = GATK4_GENOMICSDBIMPORT.out.genomicsdb.join(
GATK4_GENOMICSDBIMPORT.out.intervallist).map{
meta, genomicsdb, intervallist -> [ meta, genomicsdb, [], intervallist, [] ]
}
// Joint genotyping performed using GenotypeGVCFs
// Sort vcfs called by interval within each VCF

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