indexing longphase vcf

Author: robert-a-forsyth

modules/nf-core/longphase/phase/main.nf

@@ -239,6 +239,7 @@ workflow TUMOR_NORMAL_HAPPHASE {
             return [ meta, tumor_bam, tumor_bai, normal_bam, normal_bai ]
         }
         .join(LONGPHASE_PHASE.out.vcf)
+        .join(LONGPHASE_PHASE.out.vcf.tbi)
         .set{tumor_normal_severus}
 
     // tumor_normal_severus -> meta:       [id, paired_data, platform, sex, fiber, basecall_model]
@@ -251,7 +252,7 @@ workflow TUMOR_NORMAL_HAPPHASE {
       // Get ClairS input channel
 
     tumor_normal_severus
-        .map { meta, tumor_bam, tumor_bai, normal_bam, normal_bai, vcf ->
+        .map { meta, tumor_bam, tumor_bai, normal_bam, normal_bai, vcf, tbi ->
             def model = (!meta.clairS_model || meta.clairS_model.toString().trim() in ['', '[]']) ? clairs_modelMap.get(meta.basecall_model.toString().trim()) : meta.clairS_model
             return[meta , tumor_bam, tumor_bai, normal_bam, normal_bai,model]
         }

modules/nf-core/severus/main.nf

@@ -164,14 +164,15 @@ workflow TUMOR_ONLY_HAPPHASE {
     haplotagged_bams
         .join(SAMTOOLS_INDEX.out.bai)
         .join(LONGPHASE_PHASE.out.vcf)
-        .map{meta, hap_bam, hap_bai, vcf ->
+        .join(LONGPHASE_PHASE.out.vcf.tbi)
+        .map{meta, hap_bam, hap_bai, vcf,tbi ->
             def new_meta = [id: meta.id,
                             paired_data: meta.paired_data,
                             platform: meta.platform,
                             sex: meta.sex,
                             fiber: meta.fiber,
                             basecall_model: meta.basecall_model]
-            return[new_meta, hap_bam, hap_bai, [],[], vcf]
+            return[new_meta, hap_bam, hap_bai, [],[], vcf,tbi]
             }
         .set{ tumor_only_severus }