tabix is not needed, tbi computation is done by vep (#9821)

Author: FriederikeHanssen

subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf

@@ -3,17 +3,16 @@
 //
 
 include { ENSEMBLVEP_VEP } from '../../../modules/nf-core/ensemblvep/vep'
-include { TABIX_TABIX    } from '../../../modules/nf-core/tabix/tabix'
 
 workflow VCF_ANNOTATE_ENSEMBLVEP {
     take:
-    ch_vcf // channel: [ val(meta), path(vcf), [path(custom_file1), path(custom_file2)... (optional)]]
-    ch_fasta // channel: [ val(meta2), path(fasta) ] (optional)
-    val_genome //   value: genome to use
-    val_species //   value: species to use
-    val_cache_version //   value: cache version to use
-    ch_cache // channel: [ val(meta3), path(cache) ] (optional)
-    ch_extra_files // channel: [ path(file1), path(file2)... ] (optional)
+    ch_vcf              // channel: [ val(meta), path(vcf), [path(custom_file1), path(custom_file2)... (optional)]]
+    ch_fasta            // channel: [ val(meta2), path(fasta) ] (optional)
+    val_genome          //   value: genome to use
+    val_species         //   value: species to use
+    val_cache_version   //   value: cache version to use
+    ch_cache            // channel: [ val(meta3), path(cache) ] (optional)
+    ch_extra_files      // channel: [ path(file1), path(file2)... ] (optional)
 
     main:
     ENSEMBLVEP_VEP(
@@ -26,13 +25,11 @@ workflow VCF_ANNOTATE_ENSEMBLVEP {
         ch_extra_files,
     )
 
-    TABIX_TABIX(ENSEMBLVEP_VEP.out.vcf)
-
-    ch_vcf_tbi = ENSEMBLVEP_VEP.out.vcf.join(TABIX_TABIX.out.index, failOnDuplicate: true, failOnMismatch: true)
+    ch_vcf_tbi = ENSEMBLVEP_VEP.out.vcf.join(ENSEMBLVEP_VEP.out.tbi, failOnDuplicate: true, failOnMismatch: true)
 
     emit:
-    vcf_tbi = ch_vcf_tbi // channel: [ val(meta), path(vcf), path(tbi) ]
-    json    = ENSEMBLVEP_VEP.out.json // channel: [ val(meta), path(json) ]
-    tab     = ENSEMBLVEP_VEP.out.tab // channel: [ val(meta), path(tab) ]
+    vcf_tbi = ch_vcf_tbi                // channel: [ val(meta), path(vcf), path(tbi) ]
+    json    = ENSEMBLVEP_VEP.out.json   // channel: [ val(meta), path(json) ]
+    tab     = ENSEMBLVEP_VEP.out.tab    // channel: [ val(meta), path(tab) ]
     reports = ENSEMBLVEP_VEP.out.report // channel: [ path(html) ]
 }