Added cram output to samtools/fixmate

modules/nf-core/samtools/fixmate/main.nf

@@ -8,26 +8,49 @@ process SAMTOOLS_FIXMATE {
         'biocontainers/samtools:1.21--h50ea8bc_0' }"
 
     input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(input)
 
     output:
-    tuple val(meta), path("*.bam"), emit: bam
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("${prefix}.bam") , emit: bam , optional: true
+    tuple val(meta), path("${prefix}.cram"), emit: cram, optional: true
+    tuple val(meta), path("${prefix}.sam") , emit: sam , 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 ?: "${meta.id}"
-    if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    prefix = task.ext.prefix ?: "${meta.id}_fixmate"
+    def extension = args.contains("--output-fmt sam") ? "sam" :
+                    args.contains("--output-fmt bam") ? "bam" :
+                    args.contains("--output-fmt cram") ? "cram" :
+                    "bam"
+    if ("$input" == "${prefix}.${extension}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     samtools \\
         fixmate  \\
         $args \\
         --threads ${task.cpus-1} \\
-        $bam \\
-        ${prefix}.bam \\
+        $input \\
+        ${prefix}.${extension} \\
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}_fixmate"
+    def extension = args.contains("--output-fmt sam") ? "sam" :
+                    args.contains("--output-fmt bam") ? "bam" :
+                    args.contains("--output-fmt cram") ? "cram" :
+                    "bam"
+    if ("$input" == "${prefix}.${extension}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    """
+    touch ${prefix}.${extension}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/samtools/fixmate/meta.yml

@@ -29,28 +29,74 @@ input:
         description: |
           Groovy Map containing sample information
           e.g. [ id:'test', single_end:false ]
-    - bam:
+    - input:
         type: file
         description: BAM/CRAM/SAM file, must be sorted by name, not coordinate
         pattern: "*.{bam,cram,sam}"
+        ontologies:
+          - edam: http://edamontology.org/format_2572 # BAM
+          - edam: http://edamontology.org/format_3462 # CRAM
+          - edam: http://edamontology.org/format_2573 # SAM
 output:
   - bam:
       - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "*.bam":
-          type: file
-          description: A BAM/CRAM/SAM file with mate information added and/or proper pairs
-            recalled
-          pattern: "*.{bam,cram,sam}"
+          pattern: "*.{bam}"
+          ontologies:
+            - edam: http://edamontology.org/format_2572
+      - ${prefix}.bam:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+          pattern: "*.{bam}"
+          ontologies:
+            - edam: http://edamontology.org/format_2572
+  - cram:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+          pattern: "*.{cram}"
+          ontologies:
+            - edam: http://edamontology.org/format_3462
+      - ${prefix}.cram:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+          pattern: "*.{cram}"
+          ontologies:
+            - edam: http://edamontology.org/format_3462
+  - sam:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+          pattern: "*.{sam}"
+          ontologies:
+            - edam: http://edamontology.org/format_2573
+      - ${prefix}.sam:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+          pattern: "*.{sam}"
+          ontologies:
+            - edam: http://edamontology.org/format_2573
   - versions:
       - versions.yml:
           type: file
           description: File containing software versions
           pattern: "versions.yml"
+          ontologies: []
 authors:
   - "@sppearce"
 maintainers:
   - "@sppearce"
+  - "@GallVp"

modules/nf-core/samtools/fixmate/tests/main.nf.test

@@ -1,19 +1,23 @@
-// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
-// nf-core modules test samtools/fixmate
 nextflow_process {
 
     name "Test Process SAMTOOLS_FIXMATE"
     script "../main.nf"
     process "SAMTOOLS_FIXMATE"
+    config "./nextflow.config"
 
     tag "modules"
     tag "modules_nfcore"
     tag "samtools"
     tag "samtools/fixmate"
+    tag "samtools/sort"
 
     test("sarscov2 - bam") {
 
         when {
+            params {
+                module_args = ''
+                samtools_sort_args = ''
+            }
             process {
                 """
                 input[0] = Channel.of([
@@ -27,9 +31,85 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(file(process.out.bam[0][1]).name).match("bam") },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(
+                    bam(process.out.bam[0][1]).getReadsMD5(),
+                    process.out.versions)
+                    .match()
+                }
+            )
+        }
+    }
+
+    test("human - cram") {
+
+        setup {
+            run("SAMTOOLS_SORT") {
+                script "../../../samtools/sort/main.nf"
+                process {
+                    """
+                    input[0] = [
+                        [ id:'test', single_end:false ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true)
+                    ]
+                    input[1] = [
+                        [ id:'test' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                    ]
+                    """
+                }
+            }
+        }
+
+        when {
+            params {
+                module_args         = '--output-fmt cram'
+                samtools_sort_args  = '--template-coordinate --output-fmt cram'
+            }
+            process {
+                """
+                input[0] = SAMTOOLS_SORT.out.cram
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.cram[0][1]).name,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
+
+    }
+
+    test("human - cram - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                module_args = '--output-fmt cram'
+                samtools_sort_args = ''
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
     }
-}
+}

modules/nf-core/samtools/fixmate/tests/main.nf.test.snap

@@ -1,24 +1,75 @@
 {
-    "versions": {
+    "human - cram - stub": {
         "content": [
+            {
+                "0": [
+
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_fixmate.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+
+                ],
+                "3": [
+                    "versions.yml:md5,d1afb9aa7c14a683e2a0b8a43daa5d31"
+                ],
+                "bam": [
+
+                ],
+                "cram": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_fixmate.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "sam": [
+
+                ],
+                "versions": [
+                    "versions.yml:md5,d1afb9aa7c14a683e2a0b8a43daa5d31"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-21T06:53:59.470746689"
+    },
+    "human - cram": {
+        "content": [
+            "test_fixmate.cram",
             [
                 "versions.yml:md5,d1afb9aa7c14a683e2a0b8a43daa5d31"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-16T08:01:53.33860034"
+        "timestamp": "2025-03-21T06:53:49.930885979"
     },
-    "bam": {
+    "sarscov2 - bam": {
         "content": [
-            "test.bam"
+            "762e859a3d0ed1553655cde77665c940",
+            [
+                "versions.yml:md5,d1afb9aa7c14a683e2a0b8a43daa5d31"
+            ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-02-12T18:24:59.755324"
+        "timestamp": "2025-03-21T06:47:32.759541463"
     }
 }

modules/nf-core/samtools/fixmate/tests/nextflow.config

@@ -0,0 +1,9 @@
+process {
+    withName: 'SAMTOOLS_FIXMATE' {
+        ext.args = params.module_args
+    }
+    withName: 'SAMTOOLS_SORT' {
+        ext.args = params.samtools_sort_args
+        ext.prefix = { "${meta.id}.sorted" }
+    }
+}

modules/nf-core/samtools/markdup/tests/main.nf.test

@@ -87,4 +87,4 @@ nextflow_process {
 
     }
 
-}
+}

modules/yaml-schema.json

@@ -0,0 +1 @@
+meta-schema.json