correct mix of channels

nf-core · Oct 30, 2024 · 971667b · 971667b
1 parent c4a09e0
commit 971667b
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Showing 2 changed files with 8 additions and 7 deletions.
diff --git a/subworkflows/local/align_cellranger.nf b/subworkflows/local/align_cellranger.nf
@@ -63,7 +63,8 @@ workflow CELLRANGER_ALIGN {
 
     emit:
         ch_versions
-        cellranger_out      = CELLRANGER_COUNT.out.outs
-        cellranger_matrices = ch_matrices_raw.mix( ch_matrices_filtered )
-        star_index          = cellranger_index
+        cellranger_out               = CELLRANGER_COUNT.out.outs
+        cellranger_matrices_raw      = ch_matrices_raw
+        cellranger_matrices_filtered = ch_matrices_filtered
+        star_index                   = cellranger_index
 }
diff --git a/workflows/scrnaseq.nf b/workflows/scrnaseq.nf
@@ -135,7 +135,7 @@ workflow SCRNASEQ {
             ch_fastq
         )
         ch_versions = ch_versions.mix(KALLISTO_BUSTOOLS.out.ch_versions)
-        ch_mtx_matrices = KALLISTO_BUSTOOLS.out.counts_raw.mix( KALLISTO_BUSTOOLS.out.counts_filtered )
+        ch_mtx_matrices = ch_mtx_matrices.mix( KALLISTO_BUSTOOLS.out.counts_raw, KALLISTO_BUSTOOLS.out.counts_filtered )
         ch_txp2gene = KALLISTO_BUSTOOLS.out.txp2gene
     }
 
@@ -153,7 +153,7 @@ workflow SCRNASEQ {
         )
         ch_versions = ch_versions.mix(SCRNASEQ_ALEVIN.out.ch_versions)
         ch_multiqc_files = ch_multiqc_files.mix(SCRNASEQ_ALEVIN.out.alevin_results.map{ meta, it -> it })
-        ch_mtx_matrices = ch_mtx_matrices.mix(SCRNASEQ_ALEVIN.out.alevin_results)
+        ch_mtx_matrices = ch_mtx_matrices.mix( SCRNASEQ_ALEVIN.out.alevin_results )
     }
 
     // Run STARSolo pipeline
@@ -170,7 +170,7 @@ 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.raw_counts.mix( STARSOLO.out.filtered_counts )
+        ch_mtx_matrices = ch_mtx_matrices.mix( STARSOLO.out.raw_counts, STARSOLO.out.filtered_counts )
     }
 
     // Run cellranger pipeline
@@ -183,7 +183,7 @@ workflow SCRNASEQ {
             protocol_config['protocol']
         )
         ch_versions = ch_versions.mix(CELLRANGER_ALIGN.out.ch_versions)
-        ch_mtx_matrices = ch_mtx_matrices.mix(CELLRANGER_ALIGN.out.cellranger_matrices)
+        ch_mtx_matrices = ch_mtx_matrices.mix( CELLRANGER_ALIGN.out.cellranger_matrices_raw, CELLRANGER_ALIGN.out.cellranger_matrices_filtered )
         ch_multiqc_files = ch_multiqc_files.mix(CELLRANGER_ALIGN.out.cellranger_out.map {
             meta, outs -> outs.findAll{ it -> it.name == "web_summary.html"}
         })