Restored having index as input for check vcf step

Ensembl · Sep 24, 2023 · e25bf50 · e25bf50
1 parent cbe1ecd
commit e25bf50
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/nextflow/nf_modules/check_VCF.nf b/nextflow/nf_modules/check_VCF.nf
@@ -20,7 +20,7 @@ process checkVCF {
   errorStrategy 'ignore'
 
   input:
-  tuple val(meta), path(vcf), path(vep_config)
+  tuple val(meta), path(vcf), path(vcf_index), path(vep_config)
 
   output:
   tuple val(meta), path("*.gz", includeInputs: true), path ("*.gz.{tbi,csi}", includeInputs: true), path(vep_config)

diff --git a/nextflow/workflows/run_vep.nf b/nextflow/workflows/run_vep.nf
@@ -135,7 +135,9 @@ workflow {
         // NOTE: csi is default unless a tbi index already exists
         meta.index_type = file(vcf + ".tbi").exists() ? "tbi" : "csi"
 
-        [ meta, vcf, vep_config ]
+        vcf_index = vcf + ".${meta.index_type}"
+
+        [ meta, vcf, vcf_index, vep_config ]
     }
     .set{ ch_input }