Improve output glob for optional alignments

nf-core · Jul 27, 2023 · 7c74c5c · 7c74c5c
1 parent d591036
commit 7c74c5c
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Showing 2 changed files with 6 additions and 1 deletion.
diff --git a/modules/nf-core/centrifuge/centrifuge/main.nf b/modules/nf-core/centrifuge/centrifuge/main.nf
@@ -16,7 +16,7 @@ process CENTRIFUGE_CENTRIFUGE {
     output:
     tuple val(meta), path('*report.txt')                 , emit: report
     tuple val(meta), path('*results.txt')                , emit: results
-    tuple val(meta), path('*.sam')                       , optional: true, emit: sam
+    tuple val(meta), path('*.{sam,tab}')                 , optional: true, emit: sam
     tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz')   , optional: true, emit: fastq_mapped
     tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_unmapped
     path "versions.yml"                                  , emit: versions

diff --git a/modules/nf-core/centrifuge/centrifuge/meta.yml b/modules/nf-core/centrifuge/centrifuge/meta.yml
@@ -48,6 +48,11 @@ output:
       description: |
         File containing classification results
       pattern: "*.{results.txt}"
+  - sam:
+      type: file
+      description: |
+        Optional output file containing read alignments (SAM format )or a table of per-read hit information (TAB)s
+      pattern: "*.{sam,tab}"
   - fastq_unmapped:
       type: file
       description: Unmapped fastq files