APPLYBQSR output line specificity

modules/nf-core/gatk4spark/applybqsr/main.nf

@@ -14,16 +14,16 @@ process GATK4SPARK_APPLYBQSR {
     path  dict
 
     output:
-    tuple val(meta), path("*.bam") , emit: bam,  optional: true
-    tuple val(meta), path("*.cram"), emit: cram, optional: true
+    tuple val(meta), path("${prefix}.bam") , emit: bam,  optional: true
+    tuple val(meta), path("${prefix}.cram"), emit: cram, optional: true
     path "versions.yml"            , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     def interval_command = intervals ? "--intervals $intervals" : ""
 
     def avail_mem = 3072
@@ -52,7 +52,7 @@ process GATK4SPARK_APPLYBQSR {
     """
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.bam
     touch ${prefix}.cram

modules/nf-core/gatk4spark/applybqsr/meta.yml

@@ -1,85 +1,91 @@
 name: gatk4spark_applybqsr
 description: Apply base quality score recalibration (BQSR) to a bam file
 keywords:
-  - bam
-  - base quality score recalibration
-  - bqsr
-  - cram
-  - gatk4spark
+- bam
+- base quality score recalibration
+- bqsr
+- cram
+- gatk4spark
 tools:
-  - gatk4:
-      description: |
-        Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
-        with a primary focus on variant discovery and genotyping. Its powerful processing engine
-        and high-performance computing features make it capable of taking on projects of any size.
-      homepage: https://gatk.broadinstitute.org/hc/en-us
-      documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
-      doi: 10.1158/1538-7445.AM2017-3590
-      licence: ["Apache-2.0"]
-      identifier: ""
+- gatk4:
+    description: |
+      Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
+      with a primary focus on variant discovery and genotyping. Its powerful processing engine
+      and high-performance computing features make it capable of taking on projects of any size.
+    homepage: https://gatk.broadinstitute.org/hc/en-us
+    documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
+    doi: 10.1158/1538-7445.AM2017-3590
+    licence: ["Apache-2.0"]
+    identifier: ""
 input:
-  - - meta:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
-    - input:
-        type: file
-        description: BAM/CRAM file from alignment
-        pattern: "*.{bam,cram}"
-    - input_index:
-        type: file
-        description: BAI/CRAI file from alignment
-        pattern: "*.{bai,crai}"
-    - bqsr_table:
-        type: file
-        description: Recalibration table from gatk4_baserecalibrator
-    - intervals:
-        type: file
-        description: Bed file with the genomic regions included in the library (optional)
-  - - fasta:
-        type: file
-        description: The reference fasta file
-        pattern: "*.fasta"
-  - - fai:
-        type: file
-        description: Index of reference fasta file
-        pattern: "*.fasta.fai"
-  - - dict:
-        type: file
-        description: GATK sequence dictionary
-        pattern: "*.dict"
+- - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - input:
+      type: file
+      description: BAM/CRAM file from alignment
+      pattern: "*.{bam,cram}"
+  - input_index:
+      type: file
+      description: BAI/CRAI file from alignment
+      pattern: "*.{bai,crai}"
+  - bqsr_table:
+      type: file
+      description: Recalibration table from gatk4_baserecalibrator
+  - intervals:
+      type: file
+      description: Bed file with the genomic regions included in the library (optional)
+- - fasta:
+      type: file
+      description: The reference fasta file
+      pattern: "*.fasta"
+- - fai:
+      type: file
+      description: Index of reference fasta file
+      pattern: "*.fasta.fai"
+- - dict:
+      type: file
+      description: GATK sequence dictionary
+      pattern: "*.dict"
 output:
-  - bam:
-      - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-      - "*.bam":
-          type: file
-          description: Recalibrated BAM file
-          pattern: "*.{bam}"
-  - cram:
-      - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-      - "*.cram":
-          type: file
-          description: Recalibrated CRAM file
-          pattern: "*.{cram}"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+- bam:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+      pattern: "*.{bam}"
+  - ${prefix}.bam:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+      pattern: "*.{bam}"
+- cram:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+      pattern: "*.{cram}"
+  - ${prefix}.cram:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+      pattern: "*.{cram}"
+- versions:
+  - versions.yml:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
 authors:
-  - "@yocra3"
-  - "@FriederikeHanssen"
-  - "@maxulysse"
+- "@yocra3"
+- "@FriederikeHanssen"
+- "@maxulysse"
 maintainers:
-  - "@yocra3"
-  - "@FriederikeHanssen"
-  - "@maxulysse"
+- "@yocra3"
+- "@FriederikeHanssen"
+- "@maxulysse"

modules/nf-core/gatk4spark/applybqsr/tests/main.nf.test.snap

@@ -43,10 +43,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-06T11:47:37.292174976"
+        "timestamp": "2025-03-17T16:50:02.397152291"
     },
     "sarscov2 - cram": {
         "content": [
@@ -82,10 +82,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-06T11:48:24.575560544"
+        "timestamp": "2025-03-17T16:50:30.685886937"
     },
     "sarscov2 - bam": {
         "content": [
@@ -121,10 +121,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-06T11:46:46.042894548"
+        "timestamp": "2025-03-17T16:49:26.18719288"
     },
     "sarscov2 - bam intervals": {
         "content": [
@@ -160,9 +160,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-06T11:47:13.436442722"
+        "timestamp": "2025-03-17T16:49:49.844595108"
     }
 }