From 4d1f7652507aaa62b966a45158928ad5141fb822 Mon Sep 17 00:00:00 2001
From: Judith Ballesteros <judith.vballesteros@gmail.com>
Date: Fri, 26 Jan 2024 11:15:44 +0100
Subject: [PATCH] importing properly samtools module

---
 conf/modules.config                     |  5 +++--
 subworkflows/local/sex_determination.nf | 10 +++++-----
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 13f50f898..e1651f0fd 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -887,12 +887,12 @@ process {
     //
     // SEXDETERRMINE
     //
-    withName: SAMTOOLS_DEPTH {
+    withName: SAMTOOLS_DEPTH_SEXDETERMINE {
         tag = { "${meta1.reference}|${meta1.sample_id}_${meta1.library_id}" }
         ext.prefix = { "${meta1.sample_id}_${meta1.library_id}_samtoolsdepth" }
         ext.args = '-aa -q30 -Q30 -H'
         publishDir = [
-            enabled: false
+        enabled: false
         ]
     }
 
@@ -902,6 +902,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/sex_determine/sexdeterrmine/" },
             mode: params.publish_dir_mode,
+            pattern: '*{_sexdetermine}*',
             enabled: true
         ]
     }
diff --git a/subworkflows/local/sex_determination.nf b/subworkflows/local/sex_determination.nf
index 620bc38fc..b20c9cdd7 100644
--- a/subworkflows/local/sex_determination.nf
+++ b/subworkflows/local/sex_determination.nf
@@ -2,8 +2,8 @@
 // Run sex determine
 //
 
-include { SAMTOOLS_DEPTH } from '../../modules/nf-core/samtools/depth/main'
-include { SEXDETERRMINE } from '../../modules/nf-core/sexdeterrmine/main'
+include { SAMTOOLS_DEPTH as SAMTOOLS_DEPTH_SEXDETERMINE } from '../../modules/nf-core/samtools/depth/main'
+include { SEXDETERRMINE                                 } from '../../modules/nf-core/sexdeterrmine/main'
 
 workflow RUN_SEXDETERMINE {
 
@@ -28,9 +28,9 @@ workflow RUN_SEXDETERMINE {
                             intervals : [ meta2, bed ]
                                     }
 
-    SAMTOOLS_DEPTH(ch_samtoolsdepth_input)
-    ch_sex_determine_input = SAMTOOLS_DEPTH.out.tsv
-    ch_versions            = ch_versions.mix( SAMTOOLS_DEPTH.out.versions )
+    SAMTOOLS_DEPTH_SEXDETERMINE(ch_samtoolsdepth_input)
+    ch_sex_determine_input = SAMTOOLS_DEPTH_SEXDETERMINE.out.tsv
+    ch_versions            = ch_versions.mix( SAMTOOLS_DEPTH_SEXDETERMINE.out.versions )
 
     // Run sex determination with samtools depth input
     // Does it need a sample list file to run?