Merge branch 'dev' into fresh-nf-test

CHANGELOG.md

@@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 
 - [1669](https://github.com/nf-core/sarek/pull/1669) - Better nf-test pipeline level tests
+- [1675](https://github.com/nf-core/sarek/pull/1675) - Migrate pytest aligner tests to nf-test
 
 ### Fixed
 

tests/aligner-bwa-mem.nf.test

@@ -0,0 +1,74 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../main.nf"
+    tag "pipeline"
+    tag "pipeline_sarek"
+
+    test("Run with profile test | --aligner bwa-mem --save_reference | skip QC/recal/md") {
+
+        when {
+            params {
+                aligner = 'bwa-mem'
+                outdir = "$outputDir"
+                save_reference = true
+                skip_tools = 'baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools'
+                tools = ''
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    getRelativePath(stable_name, outputDir),
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+
+    test("Run with profile test | --aligner bwa-mem --save_reference --build_only_index") {
+
+        when {
+            params {
+                aligner = 'bwa-mem'
+                build_only_index = true
+                input = false
+                outdir = "$outputDir"
+                save_reference = true
+                tools = ''
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    getRelativePath(stable_name, outputDir),
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+}

tests/aligner-bwa-mem.nf.test.snap

@@ -0,0 +1,118 @@
+{
+    "Run with profile test | --aligner bwa-mem --save_reference | skip QC/recal/md": {
+        "content": [
+            10,
+            {
+                "BAM_TO_CRAM_MAPPING": {
+                    "samtools": 1.21
+                },
+                "BWAMEM1_MEM": {
+                    "bwa": "0.7.18-r1243-dirty",
+                    "samtools": 1.2
+                },
+                "INDEX_MERGE_BAM": {
+                    "samtools": 1.21
+                },
+                "MERGE_BAM": {
+                    "samtools": 1.21
+                },
+                "Workflow": {
+                    "nf-core/sarek": "v3.5.0dev"
+                }
+            },
+            [
+                "csv",
+                "csv/mapped.csv",
+                "pipeline_info",
+                "pipeline_info/nf_core_sarek_software_mqc_versions.yml",
+                "preprocessing",
+                "preprocessing/mapped",
+                "preprocessing/mapped/test",
+                "preprocessing/mapped/test/test.sorted.cram",
+                "preprocessing/mapped/test/test.sorted.cram.crai",
+                "reference",
+                "reference/bwa",
+                "reference/bwa/genome.amb",
+                "reference/bwa/genome.ann",
+                "reference/bwa/genome.bwt",
+                "reference/bwa/genome.pac",
+                "reference/bwa/genome.sa",
+                "reference/intervals",
+                "reference/intervals/chr22_1-40001.bed",
+                "reference/intervals/chr22_1-40001.bed.gz",
+                "reference/intervals/genome.bed",
+                "reference/intervals/genome.bed.gz"
+            ],
+            [
+                "test.sorted.cram:md5,9b21ccf9b5c61996bf48ce9dc0a108c5",
+                "test.sorted.cram.crai:md5,169697ea55e0749cc4d8312c32d73946",
+                "genome.amb:md5,1891c1de381b3a96d4e72f590fde20c1",
+                "genome.ann:md5,2df4aa2d7580639fa0fcdbcad5e2e969",
+                "genome.bwt:md5,815eded87e4cb6b0f1daab5c4d6e30af",
+                "genome.pac:md5,8569fbdb2c98c6fb16dfa73d8eacb070",
+                "genome.sa:md5,e7cff62b919448a3a3d0fe4aaf427594",
+                "chr22_1-40001.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
+                "chr22_1-40001.bed.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
+                "genome.bed:md5,a87dc7d20ebca626f65cc16ff6c97a3e",
+                "genome.bed.gz:md5,a87dc7d20ebca626f65cc16ff6c97a3e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.09.0"
+        },
+        "timestamp": "2024-10-07T10:17:55.189941"
+    },
+    "Run with profile test | --aligner bwa-mem --save_reference --build_only_index": {
+        "content": [
+            6,
+            {
+                "Workflow": {
+                    "nf-core/sarek": "v3.5.0dev"
+                }
+            },
+            [
+                "csv",
+                "multiqc",
+                "multiqc/multiqc_data",
+                "multiqc/multiqc_data/multiqc.log",
+                "multiqc/multiqc_data/multiqc_citations.txt",
+                "multiqc/multiqc_data/multiqc_data.json",
+                "multiqc/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/multiqc_data/multiqc_sources.txt",
+                "multiqc/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_sarek_software_mqc_versions.yml",
+                "reference",
+                "reference/bwa",
+                "reference/bwa/genome.amb",
+                "reference/bwa/genome.ann",
+                "reference/bwa/genome.bwt",
+                "reference/bwa/genome.pac",
+                "reference/bwa/genome.sa",
+                "reference/intervals",
+                "reference/intervals/chr22_1-40001.bed",
+                "reference/intervals/chr22_1-40001.bed.gz",
+                "reference/intervals/genome.bed",
+                "reference/intervals/genome.bed.gz"
+            ],
+            [
+                "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+                "genome.amb:md5,1891c1de381b3a96d4e72f590fde20c1",
+                "genome.ann:md5,2df4aa2d7580639fa0fcdbcad5e2e969",
+                "genome.bwt:md5,815eded87e4cb6b0f1daab5c4d6e30af",
+                "genome.pac:md5,8569fbdb2c98c6fb16dfa73d8eacb070",
+                "genome.sa:md5,e7cff62b919448a3a3d0fe4aaf427594",
+                "chr22_1-40001.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
+                "chr22_1-40001.bed.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
+                "genome.bed:md5,a87dc7d20ebca626f65cc16ff6c97a3e",
+                "genome.bed.gz:md5,a87dc7d20ebca626f65cc16ff6c97a3e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.09.0"
+        },
+        "timestamp": "2024-10-07T10:18:42.438866"
+    }
+}

tests/aligner-bwa-mem2.nf.test

@@ -0,0 +1,74 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../main.nf"
+    tag "pipeline"
+    tag "pipeline_sarek"
+
+    test("Run with profile test | --aligner bwa-mem2 --save_reference | skip QC/recal/md") {
+
+        when {
+            params {
+                aligner = 'bwa-mem2'
+                outdir = "$outputDir"
+                save_reference = true
+                skip_tools = 'baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools'
+                tools = ''
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    getRelativePath(stable_name, outputDir),
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+
+    test("Run with profile test | --aligner bwa-mem2 --save_reference --build_only_index") {
+
+        when {
+            params {
+                aligner = 'bwa-mem2'
+                build_only_index = true
+                input = false
+                outdir = "$outputDir"
+                save_reference = true
+                tools = ''
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    getRelativePath(stable_name, outputDir),
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+}

tests/aligner-bwa-mem2.nf.test.snap

@@ -0,0 +1,118 @@
+{
+    "Run with profile test | --aligner bwa-mem2 --save_reference --build_only_index": {
+        "content": [
+            6,
+            {
+                "Workflow": {
+                    "nf-core/sarek": "v3.5.0dev"
+                }
+            },
+            [
+                "csv",
+                "multiqc",
+                "multiqc/multiqc_data",
+                "multiqc/multiqc_data/multiqc.log",
+                "multiqc/multiqc_data/multiqc_citations.txt",
+                "multiqc/multiqc_data/multiqc_data.json",
+                "multiqc/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/multiqc_data/multiqc_sources.txt",
+                "multiqc/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_sarek_software_mqc_versions.yml",
+                "reference",
+                "reference/bwamem2",
+                "reference/bwamem2/genome.fasta.0123",
+                "reference/bwamem2/genome.fasta.amb",
+                "reference/bwamem2/genome.fasta.ann",
+                "reference/bwamem2/genome.fasta.bwt.2bit.64",
+                "reference/bwamem2/genome.fasta.pac",
+                "reference/intervals",
+                "reference/intervals/chr22_1-40001.bed",
+                "reference/intervals/chr22_1-40001.bed.gz",
+                "reference/intervals/genome.bed",
+                "reference/intervals/genome.bed.gz"
+            ],
+            [
+                "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+                "genome.fasta.0123:md5,d73300d44f733bcdb7c988fc3ff3e3e9",
+                "genome.fasta.amb:md5,1891c1de381b3a96d4e72f590fde20c1",
+                "genome.fasta.ann:md5,2df4aa2d7580639fa0fcdbcad5e2e969",
+                "genome.fasta.bwt.2bit.64:md5,cd4bdf496eab05228a50c45ee43c1ed0",
+                "genome.fasta.pac:md5,8569fbdb2c98c6fb16dfa73d8eacb070",
+                "chr22_1-40001.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
+                "chr22_1-40001.bed.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
+                "genome.bed:md5,a87dc7d20ebca626f65cc16ff6c97a3e",
+                "genome.bed.gz:md5,a87dc7d20ebca626f65cc16ff6c97a3e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.09.0"
+        },
+        "timestamp": "2024-10-07T10:24:11.560414"
+    },
+    "Run with profile test | --aligner bwa-mem2 --save_reference | skip QC/recal/md": {
+        "content": [
+            10,
+            {
+                "BAM_TO_CRAM_MAPPING": {
+                    "samtools": 1.21
+                },
+                "BWAMEM2_MEM": {
+                    "bwamem2": "2.2.1",
+                    "samtools": "1.19.2"
+                },
+                "INDEX_MERGE_BAM": {
+                    "samtools": 1.21
+                },
+                "MERGE_BAM": {
+                    "samtools": 1.21
+                },
+                "Workflow": {
+                    "nf-core/sarek": "v3.5.0dev"
+                }
+            },
+            [
+                "csv",
+                "csv/mapped.csv",
+                "pipeline_info",
+                "pipeline_info/nf_core_sarek_software_mqc_versions.yml",
+                "preprocessing",
+                "preprocessing/mapped",
+                "preprocessing/mapped/test",
+                "preprocessing/mapped/test/test.sorted.cram",
+                "preprocessing/mapped/test/test.sorted.cram.crai",
+                "reference",
+                "reference/bwamem2",
+                "reference/bwamem2/genome.fasta.0123",
+                "reference/bwamem2/genome.fasta.amb",
+                "reference/bwamem2/genome.fasta.ann",
+                "reference/bwamem2/genome.fasta.bwt.2bit.64",
+                "reference/bwamem2/genome.fasta.pac",
+                "reference/intervals",
+                "reference/intervals/chr22_1-40001.bed",
+                "reference/intervals/chr22_1-40001.bed.gz",
+                "reference/intervals/genome.bed",
+                "reference/intervals/genome.bed.gz"
+            ],
+            [
+                "test.sorted.cram:md5,47d93e48e806bbca9b76a72671c31256",
+                "test.sorted.cram.crai:md5,70f3ec29d6f6fc2d9fa87ada23cc3ec6",
+                "genome.fasta.0123:md5,d73300d44f733bcdb7c988fc3ff3e3e9",
+                "genome.fasta.amb:md5,1891c1de381b3a96d4e72f590fde20c1",
+                "genome.fasta.ann:md5,2df4aa2d7580639fa0fcdbcad5e2e969",
+                "genome.fasta.bwt.2bit.64:md5,cd4bdf496eab05228a50c45ee43c1ed0",
+                "genome.fasta.pac:md5,8569fbdb2c98c6fb16dfa73d8eacb070",
+                "chr22_1-40001.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
+                "chr22_1-40001.bed.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
+                "genome.bed:md5,a87dc7d20ebca626f65cc16ff6c97a3e",
+                "genome.bed.gz:md5,a87dc7d20ebca626f65cc16ff6c97a3e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.09.0"
+        },
+        "timestamp": "2024-10-07T10:23:26.446846"
+    }
+}