Change output directory and file names for bwa index

modules/nf-core/bwa/index/main.nf

@@ -1,44 +1,46 @@
 process BWA_INDEX {
-    tag "$fasta"
+    tag "${fasta}"
     // NOTE requires 5.37N memory where N is the size of the database
     // source: https://bio-bwa.sourceforge.net/bwa.shtml#8
     memory { 6.B * fasta.size() }
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d7/d7e24dc1e4d93ca4d3a76a78d4c834a7be3985b0e1e56fddd61662e047863a8a/data' :
-        'community.wave.seqera.io/library/bwa_htslib_samtools:83b50ff84ead50d0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d7/d7e24dc1e4d93ca4d3a76a78d4c834a7be3985b0e1e56fddd61662e047863a8a/data'
+        : 'community.wave.seqera.io/library/bwa_htslib_samtools:83b50ff84ead50d0'}"
 
     input:
     tuple val(meta), path(fasta)
 
     output:
-    tuple val(meta), path("bwa"), emit: index
+    tuple val(meta), path("${prefix}"), emit: index
     tuple val("${task.process}"), val('bwa'), eval('bwa 2>&1 | sed -n "s/^Version: //p"'), topic: versions, emit: versions_bwa
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def prefix = task.ext.prefix ?: "${fasta.baseName}"
-    def args   = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: meta.id ? "${meta.id}" : "${fasta.baseName}"
+    def args = task.ext.args ?: ''
+    def suffix = task.ext.suffix ?: "${fasta.baseName}"
     """
-    mkdir bwa
+    mkdir ${prefix}
     bwa \\
         index \\
-        $args \\
-        -p bwa/${prefix} \\
-        $fasta
+        ${args} \\
+        -p ${prefix}/${suffix} \\
+        ${fasta}
     """
 
     stub:
-    def prefix = task.ext.prefix ?: "${fasta.baseName}"
+    prefix = task.ext.prefix ?: meta.id ? "${meta.id}" : "${fasta.baseName}"
+    def suffix = task.ext.suffix ?: "${fasta.baseName}"
     """
-    mkdir bwa
-    touch bwa/${prefix}.amb
-    touch bwa/${prefix}.ann
-    touch bwa/${prefix}.bwt
-    touch bwa/${prefix}.pac
-    touch bwa/${prefix}.sa
+    mkdir ${prefix}
+    touch ${prefix}/${suffix}.amb
+    touch ${prefix}/${suffix}.ann
+    touch ${prefix}/${suffix}.bwt
+    touch ${prefix}/${suffix}.pac
+    touch ${prefix}/${suffix}.sa
     """
 }

modules/nf-core/bwa/index/meta.yml

@@ -33,13 +33,13 @@ output:
           type: map
           description: |
             Groovy Map containing reference information.
-            e.g. [ id:'test', single_end:false ]
-      - bwa:
-          type: map
+            e.g. [ id:'test' ]
+      - ${prefix}:
+          type: directory
           description: |
-            Groovy Map containing reference information.
+            Directory containing bwa index files.
             e.g. [ id:'test', single_end:false ]
-          pattern: "*.{amb,ann,bwt,pac,sa}"
+          pattern: "${prefix}/*.{amb,ann,bwt,pac,sa}"
           ontologies:
             - edam: "http://edamontology.org/data_3210" # Genome index
   versions_bwa:
@@ -69,3 +69,5 @@ authors:
 maintainers:
   - "@maxulysse"
   - "@gallvp"
+contributor:
+  - "@pmoris"

modules/nf-core/parabricks/fq2bam/tests/nextflow.config

@@ -1,11 +1,9 @@
 process {
-
     withName: 'PARABRICKS_FQ2BAM' {
         ext.args = params.module_args
     }
 
     withName: 'BWA_INDEX' {
-        ext.prefix = params.bwa_prefix
+        ext.suffix = params.bwa_prefix
     }
-
 }

modules/nf-core/svaba/tests/nextflow.config

@@ -1,6 +1,6 @@
 process {
     withName: BWA_INDEX {
     // Note that this tool requires the bwa index files to be of the format genome.fasta.amb
-        ext.prefix = { "${fasta}" }
+        ext.suffix = { "${fasta}" }
     }
 }

subworkflows/nf-core/fastq_align_bwa/tests/main.nf.test.snap

@@ -8,7 +8,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.bam:md5,5dbdcfdba65fac634dcbb6984cffe2c4"
+                        "test.bam:md5,58251bd54a233f5a794aaac72b3d189b"
                     ]
                 ],
                 "1": [
@@ -17,7 +17,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.sorted.bam:md5,ba4b90f87517a16a6ae6142f37a75d79"
+                        "test.sorted.bam:md5,ecabaa3ae3ea323628ca98f1d2ffc9e3"
                     ]
                 ],
                 "2": [
@@ -77,7 +77,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.sorted.bam:md5,ba4b90f87517a16a6ae6142f37a75d79"
+                        "test.sorted.bam:md5,ecabaa3ae3ea323628ca98f1d2ffc9e3"
                     ]
                 ],
                 "bam_orig": [
@@ -86,7 +86,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.bam:md5,5dbdcfdba65fac634dcbb6984cffe2c4"
+                        "test.bam:md5,58251bd54a233f5a794aaac72b3d189b"
                     ]
                 ],
                 "csi": [
@@ -126,9 +126,9 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-02-03T11:20:05.312197328"
+        "timestamp": "2026-02-12T11:41:40.244336788"
     },
     "fastq_align_bwa_single_end": {
         "content": [
@@ -139,7 +139,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.bam:md5,f7af092ddd5203f647ba96b926392c3e"
+                        "test.bam:md5,8adf507b66fcc54f37bbd356fcef8e04"
                     ]
                 ],
                 "1": [
@@ -148,7 +148,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.sorted.bam:md5,c406a43adde2d9673e71d8a8c7db7cfd"
+                        "test.sorted.bam:md5,710bd6acfd07f0d191dc73b81402bda7"
                     ]
                 ],
                 "2": [
@@ -208,7 +208,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.sorted.bam:md5,c406a43adde2d9673e71d8a8c7db7cfd"
+                        "test.sorted.bam:md5,710bd6acfd07f0d191dc73b81402bda7"
                     ]
                 ],
                 "bam_orig": [
@@ -217,7 +217,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.bam:md5,f7af092ddd5203f647ba96b926392c3e"
+                        "test.bam:md5,8adf507b66fcc54f37bbd356fcef8e04"
                     ]
                 ],
                 "csi": [
@@ -257,8 +257,8 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-02-03T11:19:56.892854959"
+        "timestamp": "2026-02-12T11:41:30.707612915"
     }
 }