fix tbi reference

robert-a-forsyth · robert-a-forsyth · commit c4ee1a65ff6b · 2025-09-11T14:28:14.000+02:00
diff --git a/subworkflows/local/tumor_normal_happhase.nf b/subworkflows/local/tumor_normal_happhase.nf
@@ -239,7 +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)
+        .join(LONGPHASE_PHASE.out.tbi)
         .set{tumor_normal_severus}
 
     // tumor_normal_severus -> meta:       [id, paired_data, platform, sex, fiber, basecall_model]
diff --git a/subworkflows/local/tumor_only_happhase.nf b/subworkflows/local/tumor_only_happhase.nf
@@ -164,7 +164,7 @@ workflow TUMOR_ONLY_HAPPHASE {
     haplotagged_bams
         .join(SAMTOOLS_INDEX.out.bai)
         .join(LONGPHASE_PHASE.out.vcf)
-        .join(LONGPHASE_PHASE.out.vcf.tbi)
+        .join(LONGPHASE_PHASE.out.tbi)
         .map{meta, hap_bam, hap_bai, vcf,tbi ->
             def new_meta = [id: meta.id,
                             paired_data: meta.paired_data,

Original file line number	Diff line number	Diff line change
`@@ -239,7 +239,7 @@ workflow TUMOR_NORMAL_HAPPHASE {`
`239`	`239`	`return [ meta, tumor_bam, tumor_bai, normal_bam, normal_bai ]`
`240`	`240`	`}`
`241`	`241`	`.join(LONGPHASE_PHASE.out.vcf)`
`242`		`- .join(LONGPHASE_PHASE.out.vcf.tbi)`
	`242`	`+ .join(LONGPHASE_PHASE.out.tbi)`
`243`	`243`	`.set{tumor_normal_severus}`
`244`	`244`
`245`	`245`	`// tumor_normal_severus -> meta: [id, paired_data, platform, sex, fiber, basecall_model]`