refactor: use simple names and extension globbing

CHANGELOG.md

@@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
-.
+- [PR #79](https://github.com/nf-core/fastquorum/pull/79) - Publish aligned consensus bai file
 
 ## [[1.0.1]](https://github.com/nf-core/fastquorum/releases/tag/1.0.1) -- 2024-09-10
 

conf/modules.config

@@ -56,30 +56,23 @@ process {
         ]
     }
 
-    withName: '.*FASTQTOBAM' {
+    withName: 'FASTQTOBAM' {
         publishDir = [
             path: { "${params.outdir}/preprocessing/fastqtobam/${meta.id}" },
             mode: params.publish_dir_mode,
             pattern: '*.unmapped.bam'
         ]
     }
 
-    withName: '.*ALIGN_RAW_BAM' {
+    withName: 'ALIGN_RAW_BAM' {
         publishDir = [
-            [
-                path: { "${params.outdir}/preprocessing/align_raw_bam/${meta.id}" },
-                mode: params.publish_dir_mode,
-                pattern: '*.mapped.bam'
-            ],
-            [
-                path: { "${params.outdir}/preprocessing/align_raw_bam/${meta.id}" },
-                mode: params.publish_dir_mode,
-                pattern: '*.mapped.bam.bai'
-            ]
+            path: { "${params.outdir}/preprocessing/align_raw_bam/${meta.id}" },
+            mode: params.publish_dir_mode,
+            pattern: '*.mapped.{bam, bam.bai}'
         ]
     }
 
-    withName: '.*MERGE_BAM' {
+    withName: 'MERGE_BAM' {
         ext.args = '--template-coordinate'
         publishDir = [
             path: { "${params.outdir}/preprocessing/merged/${meta.id}" },
@@ -89,7 +82,7 @@ process {
     }
 
     /* This can be removed when https://github.com/samtools/samtools/pull/2062 is merged */
-    withName: '.*SORTBAM' {
+    withName: 'SORTBAM' {
         ext.args = '--sort-order TemplateCoordinate'
         ext.prefix = { "${meta.id}.sorted" }
         publishDir = [
@@ -99,7 +92,7 @@ process {
         ]
     }
 
-    withName: '.*GROUPREADSBYUMI' {
+    withName: 'GROUPREADSBYUMI' {
         publishDir = [
             [
                 path: { "${params.outdir}/grouping/groupreadsbyumi/${meta.id}" },
@@ -115,54 +108,40 @@ process {
     }
 
     if (params.duplex_seq) {
-        withName: '.*COLLECTDUPLEXSEQMETRICS' {
+        withName: 'COLLECTDUPLEXSEQMETRICS' {
             publishDir = [
-                [
-                    path: { "${params.outdir}/metrics/duplex_seq/${meta.id}" },
-                    mode: params.publish_dir_mode,
-                    pattern: '*duplex_seq_metrics*.txt'
-                ],
-                [
-                    path: { "${params.outdir}/metrics/duplex_seq/${meta.id}" },
-                    mode: params.publish_dir_mode,
-                    pattern: '*duplex_seq_metrics*.pdf'
-                ]
+                path: { "${params.outdir}/metrics/duplex_seq/${meta.id}" },
+                mode: params.publish_dir_mode,
+                pattern: '*duplex_seq_metrics*.{txt, pdf}'
             ]
         }
     }
 
-    withName: '.*CALLDDUPLEXCONSENSUSREADS|.*CALLMOLECULARCONSENSUSREADS' {
+    withName: 'CALLDDUPLEXCONSENSUSREADS|CALLMOLECULARCONSENSUSREADS' {
         publishDir = [
             path: { "${params.outdir}/consensus_calling/called/${meta.id}" },
             mode: params.publish_dir_mode,
             pattern: '*.cons.unmapped.bam'
         ]
     }
 
-    withName: '.*CALLANDFILTERDUPLEXCONSENSUSREADS|.*CALLANDFILTERMOLECULARCONSENSUSREADS|.*FILTERCONSENSUSREADS' {
+    withName: 'CALLANDFILTERDUPLEXCONSENSUSREADS|CALLANDFILTERMOLECULARCONSENSUSREADS|FILTERCONSENSUSREADS' {
         publishDir = [
-            [
-                path: { "${params.outdir}/consensus_filtering/filtered/${meta.id}" },
-                mode: params.publish_dir_mode,
-                pattern: '*.cons.filtered.bam'
-            ],
-            [
-                path: { "${params.outdir}/consensus_filtering/filtered/${meta.id}" },
-                mode: params.publish_dir_mode,
-                pattern: '*.cons.filtered.bam.bai'
-            ]
+            path: { "${params.outdir}/consensus_filtering/filtered/${meta.id}" },
+            mode: params.publish_dir_mode,
+            pattern: '*.cons.filtered.{bam, bam.bai}'
         ]
     }
 
     withName:'FILTERCONSENSUSREADS' {
         memory = { check_max( 12.GB * task.attempt, 'memory' ) }
     }
 
-    withName: '.*ALIGN_CONSENSUS_BAM' {
+    withName: 'ALIGN_CONSENSUS_BAM' {
         publishDir = [
             path: { "${params.outdir}/filtering/align_consensus_bam/${meta.id}" },
             mode: params.publish_dir_mode,
-            pattern: '*.mapped.bam'
+            pattern: '*.mapped.{bam, bam.bai}'
         ]
     }