Add config for publishing pseudo-alignment files

Author: drpatelh

workflows/rnaseq/nextflow.config

@@ -338,7 +338,38 @@ if (!params.skip_alignment && params.aligner == 'star_rsem') {
     }
 }
 
+//
+// Pseudo-alignment options
+//
+
 if (!params.skip_pseudo_alignment && params.pseudo_aligner) {
+    process {
+        withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:TX2GENE' {
+            publishDir = [
+                path: { "${params.outdir}/${params.pseudo_aligner}" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+
+        withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:TXIMPORT' {
+            ext.prefix = { "${quant_type}.merged" }
+            publishDir = [
+                path: { "${params.outdir}/${params.pseudo_aligner}" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+
+        withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_.*' {
+            publishDir = [
+                path: { "${params.outdir}/${params.pseudo_aligner}" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+    }
+
     if (!params.skip_qc & !params.skip_deseq2_qc) {
         process {
             withName: 'DESEQ2_QC_PSEUDO' {