From 041994041df1c1399975ff2debe8a497f229af49 Mon Sep 17 00:00:00 2001
From: shihabdider <shihabdider@gmail.com>
Date: Mon, 13 May 2024 12:44:31 -0400
Subject: [PATCH] refactor: update sage modules

---
 modules/local/sage/germline/main.nf | 2 +-
 modules/local/sage/somatic/main.nf  | 2 +-
 subworkflows/local/bam_sage/main.nf | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/local/sage/germline/main.nf b/modules/local/sage/germline/main.nf
index 41ab01f..41bad78 100644
--- 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
index 6b251f9..47effb6 100644
--- 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
index 00ee629..a11518d 100644
--- 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