have outputs separated

nf-core · Oct 30, 2024 · 7230095 · 7230095
1 parent cb67797
commit 7230095
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Showing 2 changed files with 8 additions and 10 deletions.
diff --git a/subworkflows/local/starsolo.nf b/subworkflows/local/starsolo.nf
@@ -54,16 +54,12 @@ workflow STARSOLO {
     )
     ch_versions = ch_versions.mix(STAR_ALIGN.out.versions)
 
-    // generate channel of star counts with correct metadata
-    ch_star_counts =
-        STAR_ALIGN.out.raw_counts.map{ meta, files -> [meta + [input_type: 'raw'], files] }
-        .mix( STAR_ALIGN.out.filtered_counts.map{ meta, files -> [meta + [input_type: 'filtered'], files] } )
-
-
     emit:
     ch_versions
     // get rid of meta for star index
-    star_result = STAR_ALIGN.out.tab
-    star_counts = ch_star_counts
-    for_multiqc = STAR_ALIGN.out.log_final.map{ meta, it -> it }
+    star_result     = STAR_ALIGN.out.tab
+    star_counts     = STAR_ALIGN.out.counts
+    raw_counts      = STAR_ALIGN.out.raw_counts
+    filtered_counts = STAR_ALIGN.out.filtered_counts
+    for_multiqc     = STAR_ALIGN.out.log_final.map{ meta, it -> it }
 }
diff --git a/workflows/scrnaseq.nf b/workflows/scrnaseq.nf
@@ -170,7 +170,9 @@ workflow SCRNASEQ {
         )
         ch_versions = ch_versions.mix(STARSOLO.out.ch_versions)
         ch_multiqc_files = ch_multiqc_files.mix(STARSOLO.out.for_multiqc)
-        ch_mtx_matrices = STARSOLO.out.star_counts
+        ch_mtx_matrices =
+            STARSOLO.out.raw_counts.map{ meta, files -> [meta + [input_type: 'raw'], files] }
+            .mix( STARSOLO.out.filtered_counts.map{ meta, files -> [meta + [input_type: 'filtered'], files] } )
     }
 
     // Run cellranger pipeline