update kallistobustools count output list (#5110)

* update kallistobustools count output list * update stub snapshot as new output channels are now emitted
nf-core · Mar 18, 2024 · 9d3e489 · 9d3e489
1 parent 92ca535
commit 9d3e489
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Showing 3 changed files with 41 additions and 5 deletions.
diff --git a/modules/nf-core/kallistobustools/count/main.nf b/modules/nf-core/kallistobustools/count/main.nf
@@ -17,9 +17,11 @@ process KALLISTOBUSTOOLS_COUNT {
     val   workflow_mode
 
     output:
-    tuple val(meta), path ("*.count")   , emit: count
-    path "versions.yml"                 , emit: versions
-    path "*.count/*/*.mtx"              , emit: matrix //Ensure that kallisto finished and produced outputs
+    tuple val(meta), path ("*.count")                  , emit: count
+    tuple val(meta), path ("*.count/counts_unfiltered"), emit: raw_counts
+    tuple val(meta), path ("*.count/counts_filtered")  , emit: filtered_counts, optional: true
+    path "versions.yml"                                , emit: versions
+    path "*.count/*/*.mtx"                             , emit: matrix //Ensure that kallisto finished and produced outputs
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/modules/nf-core/kallistobustools/count/meta.yml b/modules/nf-core/kallistobustools/count/meta.yml
@@ -58,6 +58,14 @@ output:
       type: file
       description: kb count output folder
       pattern: "*.{count}"
+  - raw_counts:
+      type: file
+      description: kb raw counts output folder
+      pattern: "*.{count}/counts_unfiltered"
+  - filtered_counts:
+      type: file
+      description: kb filtered counts output folder
+      pattern: "*.{count}/counts_filtered"
   - versions:
       type: file
       description: File containing software versions

diff --git a/modules/nf-core/kallistobustools/count/tests/main.nf.test.snap b/modules/nf-core/kallistobustools/count/tests/main.nf.test.snap