refactor: update sage modules

mskilab-org · May 13, 2024 · 0419940 · 0419940
1 parent f27a76c
commit 0419940
Show file tree

Hide file tree

Showing 3 changed files with 4 additions and 4 deletions.
diff --git a/modules/local/sage/germline/main.nf b/modules/local/sage/germline/main.nf
@@ -17,7 +17,7 @@ process SAGE_GERMLINE {
     path(panel_bed)
     path(high_confidence_bed)
 
-    output
+    output:
     tuple val(meta), path('*.sage.germline.vcf.gz'), path('*.sage.germline.vcf.gz.tbi'), emit: vcf
     path "versions.yml"                                     , emit: versions
 

diff --git a/modules/local/sage/somatic/main.nf b/modules/local/sage/somatic/main.nf
@@ -17,7 +17,7 @@ process SAGE_SOMATIC {
     path(panel_bed)
     path(high_confidence_bed)
 
-    output
+    output:
     tuple val(meta), path('*.sage.somatic.vcf.gz'), path('*.sage.somatic.vcf.gz.tbi'), emit: vcf
     path "versions.yml"                                     , emit: versions
 

diff --git a/subworkflows/local/bam_sage/main.nf b/subworkflows/local/bam_sage/main.nf
@@ -2,8 +2,8 @@
 // BAM SAGE
 //
 
-include { SAGE_SOMATIC } from '../../../modules/local/somatic/sage/main.nf'
-include { SAGE_GERMLINE } from '../../../modules/local/somatic/germline/main.nf'
+include { SAGE_SOMATIC } from '../../../modules/local/sage/somatic/main.nf'
+include { SAGE_GERMLINE } from '../../../modules/local/sage/germline/main.nf'
 
 workflow BAM_SAGE {
     // defining inputs