add more stubs gatk4

modules/nf-core/gatk4/condensedepthevidence/main.nf

@@ -50,4 +50,16 @@ process GATK4_CONDENSEDEPTHEVIDENCE {
         gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo "" | gzip > ${prefix}.rd.txt.gz
+    touch ${prefix}.rd.txt.gz.tbi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
 }

modules/nf-core/gatk4/condensedepthevidence/meta.yml

@@ -11,50 +11,61 @@ tools:
       tool_dev_url: "https://github.com/broadinstitute/gatk"
       doi: "10.1158/1538-7445.AM2017-3590"
       licence: ["BSD-3-clause"]
+      identifier: ""
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - depth_evidence:
-      type: file
-      description: The depth evidence file
-      pattern: "*.rd.txt.gz"
-  - depth_evidence_index:
-      type: file
-      description: The index of the depth evidence file
-      pattern: "*.rd.txt.gz.tbi"
-  - fasta:
-      type: file
-      description: Reference FASTA file needed when the input is a CRAM file
-      pattern: "*.{fasta,fa}"
-  - fasta_fai:
-      type: file
-      description: Index of the reference FASTA file needed when the input is a CRAM file
-      pattern: "*.fai"
-  - dict:
-      type: file
-      description: Sequence dictionary of the reference FASTA file needed when the input is a CRAM file
-      pattern: "*.dict"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - depth_evidence:
+        type: file
+        description: The depth evidence file
+        pattern: "*.rd.txt.gz"
+    - depth_evidence_index:
+        type: file
+        description: The index of the depth evidence file
+        pattern: "*.rd.txt.gz.tbi"
+  - - fasta:
+        type: file
+        description: Reference FASTA file needed when the input is a CRAM file
+        pattern: "*.{fasta,fa}"
+  - - fasta_fai:
+        type: file
+        description: Index of the reference FASTA file needed when the input is a CRAM
+          file
+        pattern: "*.fai"
+  - - dict:
+        type: file
+        description: Sequence dictionary of the reference FASTA file needed when the
+          input is a CRAM file
+        pattern: "*.dict"
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
   - condensed_evidence:
-      type: file
-      description: The condensed depth evidence
-      pattern: "*.rd.txt.gz"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.rd.txt.gz":
+          type: file
+          description: The condensed depth evidence
+          pattern: "*.rd.txt.gz"
   - condensed_evidence_index:
-      type: file
-      description: The condensed depth evidence
-      pattern: "*.rd.txt.gz.tbi"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.rd.txt.gz.tbi":
+          type: file
+          description: The condensed depth evidence
+          pattern: "*.rd.txt.gz.tbi"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@nvnieuwk"
 maintainers:

modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test

@@ -41,4 +41,33 @@ nextflow_process {
         }
     }
 
+    test("test-gatk4-condensdepthevidence - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/condensedepthevidence/testN.rd.txt.gz", checkIfExists: true),
+				    file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/condensedepthevidence/testN.rd.txt.gz.tbi", checkIfExists: true)
+				]
+				input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+				input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+				input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match()
+				}
+            )
+        }
+    }
+
 }

modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test.snap

@@ -1,4 +1,57 @@
 {
+    "test-gatk4-condensdepthevidence - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.rd.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.rd.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,d1d29007b92a10b3e50bdd25335013a8"
+                ],
+                "condensed_evidence": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.rd.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "condensed_evidence_index": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.rd.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d1d29007b92a10b3e50bdd25335013a8"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-20T10:42:07.848497"
+    },
     "test-gatk4-condensdepthevidence": {
         "content": [
             [

modules/nf-core/gatk4/fastqtosam/main.nf

@@ -42,4 +42,15 @@ process GATK4_FASTQTOSAM {
         gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
 }

modules/nf-core/gatk4/fastqtosam/meta.yml

@@ -7,36 +7,44 @@ keywords:
   - gatk4
 tools:
   - gatk4:
-      description: Genome Analysis Toolkit (GATK4) 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.
+      description: Genome Analysis Toolkit (GATK4) 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
       tool_dev_url: https://github.com/broadinstitute/gatk
       doi: "10.1158/1538-7445.AM2017-3590"
       licence: ["MIT"]
+      identifier: ""
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
-      pattern: "*.fastq.gz"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: file
+        description: List of input FastQ files of size 1 and 2 for single-end and paired-end
+          data, respectively.
+        pattern: "*.fastq.gz"
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - bam:
-      type: file
-      description: Converted BAM file
-      pattern: "*.bam"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.bam":
+          type: file
+          description: Converted BAM file
+          pattern: "*.bam"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@ntoda03"
 maintainers:

modules/nf-core/gatk4/fastqtosam/tests/main.nf.test

@@ -44,7 +44,6 @@ nextflow_process {
 				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
 				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
 				]
-
                 """
             }
         }
@@ -61,4 +60,27 @@ nextflow_process {
         }
     }
 
+    test("test-gatk4-fastqtosam-single-end - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:true ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+				]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match()
+				}
+            )
+        }
+    }
+
 }

modules/nf-core/gatk4/fastqtosam/tests/main.nf.test.snap

@@ -1,4 +1,39 @@
 {
+    "test-gatk4-fastqtosam-single-end - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ac3f2cf1b686e56d72f1dd4a5977f7ab"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ac3f2cf1b686e56d72f1dd4a5977f7ab"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-20T10:43:37.316141"
+    },
     "test-gatk4-fastqtosam-single-end": {
         "content": [
             "e6a4aa204d980e177a0458596f0a70ac",

modules/nf-core/gatk4/gatherpileupsummaries/main.nf

@@ -44,4 +44,15 @@ process GATK4_GATHERPILEUPSUMMARIES {
         gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.pileups.table
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
 }