Disable metaQuast ref download module (storage and compute intensive).

Rename decontaminated.txt.
EBI-Metagenomics · May 30, 2024 · 902fb5b · 902fb5b
1 parent 988ca49
commit 902fb5b
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Showing 3 changed files with 7 additions and 4 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -8,8 +8,8 @@ on:
     types: [published]
 
 env:
-    NXF_ANSI_LOG: false
-    NFTEST_VER: "0.8.4"
+  NXF_ANSI_LOG: false
+  NFTEST_VER: "0.8.4"
 
 jobs:
   test:

diff --git a/conf/modules.config b/conf/modules.config
@@ -288,6 +288,9 @@ process {
                 }
             ]
         ]
+        // Disable Quast reference download
+        // NOTICE: Maximum number of references (--max-ref-number) is set to 0, search in SILVA 16S rRNA database is disabled //
+        ext.args = "--max-ref-num 0"
     }
 
     withName: 'PUBLISH_DECONTAMINATED' {

diff --git a/modules/local/publish_decontaminated.nf b/modules/local/publish_decontaminated.nf
@@ -4,10 +4,10 @@ process PUBLISH_DECONTAMINATED {
     tuple val(meta), path(decontaminated_contigs)
 
     output:
-    path("decontaminated.txt")
+    path("${meta.id}.txt")
 
     script:
     """
-    mv ${decontaminated_contigs} decontaminated.txt
+    mv ${decontaminated_contigs} ${meta.id}.txt
     """
 }