fix naming

nf-core · Dec 10, 2024 · 0b144ff · 0b144ff
1 parent d28c92f
commit 0b144ff
Show file tree

Hide file tree

Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/subworkflows/local/bam_variant_calling_somatic_all/main.nf b/subworkflows/local/bam_variant_calling_somatic_all/main.nf
@@ -248,7 +248,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL {
     )
 
     emit:
-    indexcov_output
+    out_indexcov
     out_msisensorpro
     vcf_all
     vcf_freebayes

diff --git a/workflows/sarek/main.nf b/workflows/sarek/main.nf
@@ -801,8 +801,8 @@ workflow SAREK {
         reports = reports.mix(VCF_QC_BCFTOOLS_VCFTOOLS.out.vcftools_tstv_counts.collect{ meta, counts -> [ counts ] })
         reports = reports.mix(VCF_QC_BCFTOOLS_VCFTOOLS.out.vcftools_tstv_qual.collect{ meta, qual -> [ qual ] })
         reports = reports.mix(VCF_QC_BCFTOOLS_VCFTOOLS.out.vcftools_filter_summary.collect{ meta, summary -> [ summary ] })
-        reports = reports.mix(BAM_VARIANT_CALLING_GERMLINE_ALL.out.indexcov_output.collect{ meta, indexcov -> indexcov.flatten() })
-        reports = reports.mix(BAM_VARIANT_CALLING_SOMATIC_ALL.out.indexcov_output.collect{ meta, indexcov -> indexcov.flatten() })
+        reports = reports.mix(BAM_VARIANT_CALLING_GERMLINE_ALL.out.out_indexcov.collect{ meta, indexcov -> indexcov.flatten() })
+        reports = reports.mix(BAM_VARIANT_CALLING_SOMATIC_ALL.out.out_indexcov.collect{ meta, indexcov -> indexcov.flatten() })
 
         CHANNEL_VARIANT_CALLING_CREATE_CSV(vcf_to_annotate, params.outdir)