Merge branch 'master' into nf-test/atlas_pmd

modules/nf-core/atlas/call/meta.yml

@@ -12,7 +12,7 @@ tools:
       documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
       tool_dev_url: "https://bitbucket.org/wegmannlab/atlas"
       doi: "10.1101/105346"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
@@ -48,7 +48,7 @@ input:
       description: Optional tab separated text file containing 1-based list of known alleles. See atlas call documentation.
       pattern: "*.{txt.tsv}"
   - method:
-      type: character
+      type: string
       description: Which variant calling algorithm to use. Some may require additional parameters supplied via ext.args. Check atlas documentation.
       pattern: "MLE|Bayesian|allelePresence|randomBase|majorityBase"
 output:
@@ -61,7 +61,7 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  - bam:
+  - vcf:
       type: file
       description: VCF file with variant calls
       pattern: "*.vcf.gz"

modules/nf-core/atlas/call/tests/main.nf.test

@@ -0,0 +1,46 @@
+
+nextflow_process {
+
+    name "Test Process ATLAS_CALL"
+    script "../main.nf"
+    process "ATLAS_CALL"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "atlas"
+    tag "atlas/call"
+
+    test("test-atlas-call") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+				    [],
+				    []
+				]
+				input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+				input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+				input[3] = []
+				input[4] = 'randomBase'
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					path(process.out.vcf[0][1]).vcf.summary,
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}

modules/nf-core/atlas/call/tests/main.nf.test.snap

@@ -0,0 +1,15 @@
+{
+    "test-atlas-call": {
+        "content": [
+            "VcfFile [chromosomes=[MT192765.1], sampleCount=1, variantCount=12674, phased=true, phasedAutodetect=true]",
+            [
+                "versions.yml:md5,abad4c906071792f8a5270fdb143fc4e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T15:48:22.930389"
+    }
+}

modules/nf-core/atlas/recal/meta.yml

@@ -1,15 +1,16 @@
 name: "atlas_recal"
-description: gives an estimation of the sequencing bias based on known invariant sites
+description: Gives an estimation of the sequencing bias based on known invariant sites
 keywords:
   - sequencing_bias
   - ATLAS
+  - bias
 tools:
   - "atlas":
       description: "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity"
       homepage: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
       documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
       doi: "10.1101/105346"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map

modules/nf-core/atlas/recal/tests/main.nf.test

@@ -0,0 +1,44 @@
+
+nextflow_process {
+
+    name "Test Process ATLAS_RECAL"
+    script "../main.nf"
+    process "ATLAS_RECAL"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "atlas"
+    tag "atlas/recal"
+
+    test("test-atlas-recal") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+				    [],
+				    []
+				]
+				input[1] = []
+				input[2] = []
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					file(process.out.recal_patterns[0][1]).readLines()[0],
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}

modules/nf-core/atlas/recal/tests/main.nf.test.snap

@@ -0,0 +1,15 @@
+{
+    "test-atlas-recal": {
+        "content": [
+            "readGroup\tmate\tmodel\tquality\tposition\tcontext",
+            [
+                "versions.yml:md5,69864cf23ffc5b0559af20e0675c4290"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T15:57:16.06295"
+    }
+}

modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test

@@ -0,0 +1,37 @@
+
+nextflow_process {
+
+    name "Test Process BAM2FASTX_BAM2FASTQ"
+    script "../main.nf"
+    process "BAM2FASTX_BAM2FASTQ"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bam2fastx"
+    tag "bam2fastx/bam2fastq"
+
+    test("test-bam2fastx-bam2fastq") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test' ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam.pbi', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match()
+				}
+            )
+        }
+    }
+
+}

modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test.snap

@@ -0,0 +1,35 @@
+{
+    "test-bam2fastx-bam2fastq": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fastq.gz:md5,8abf16176fd1625998ee28590e1039b1"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,1b954947255d9b2ad16d2c523258cceb"
+                ],
+                "fastq": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fastq.gz:md5,8abf16176fd1625998ee28590e1039b1"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,1b954947255d9b2ad16d2c523258cceb"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T06:30:10.25178642"
+    }
+}

modules/nf-core/bamtools/stats/tests/main.nf.test

@@ -0,0 +1,35 @@
+
+nextflow_process {
+
+    name "Test Process BAMTOOLS_STATS"
+    script "../main.nf"
+    process "BAMTOOLS_STATS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bamtools"
+    tag "bamtools/stats"
+
+    test("test-bamtools-stats") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

modules/nf-core/bamtools/stats/tests/main.nf.test.snap

@@ -0,0 +1,37 @@
+{
+    "test-bamtools-stats": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam.stats:md5,b7c3f01682673a652d664a2889b15b66"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,cdecc135c35467721cc72a58b542323b"
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam.stats:md5,b7c3f01682673a652d664a2889b15b66"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,cdecc135c35467721cc72a58b542323b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T15:23:51.167984"
+    }
+}

tests/config/pytest_modules.yml

@@ -25,30 +25,18 @@ ataqv/ataqv:
 ataqv/mkarv:
   - modules/nf-core/ataqv/mkarv/**
   - tests/modules/nf-core/ataqv/mkarv/**
-atlas/call:
-  - modules/nf-core/atlas/call/**
-  - tests/modules/nf-core/atlas/call/**
-atlas/recal:
-  - modules/nf-core/atlas/recal/**
-  - tests/modules/nf-core/atlas/recal/**
 atlas/splitmerge:
   - modules/nf-core/atlas/splitmerge/**
   - tests/modules/nf-core/atlas/splitmerge/**
 authentict/deam2cont:
   - modules/nf-core/authentict/deam2cont/**
   - tests/modules/nf-core/authentict/deam2cont/**
-bam2fastx/bam2fastq:
-  - modules/nf-core/bam2fastx/bam2fastq/**
-  - tests/modules/nf-core/bam2fastx/bam2fastq/**
 bamtools/convert:
   - modules/nf-core/bamtools/convert/**
   - tests/modules/nf-core/bamtools/convert/**
 bamtools/split:
   - modules/nf-core/bamtools/split/**
   - tests/modules/nf-core/bamtools/split/**
-bamtools/stats:
-  - modules/nf-core/bamtools/stats/**
-  - tests/modules/nf-core/bamtools/stats/**
 bamutil/trimbam:
   - modules/nf-core/bamutil/trimbam/**
   - tests/modules/nf-core/bamutil/trimbam/**