Merge branch 'master' into nf-test/picard_liftovervcf

nf-core · Aug 26, 2024 · a12f189 · a12f189
2 parents 7cd5b0c + f5bc694
commit a12f189
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diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -646,6 +646,8 @@ jobs:
 
       - name: Install nf-test
         uses: nf-core/setup-nf-test@v1
+        with:
+          version: ${{ env.NFTEST_VER }}
 
       - name: Setup apptainer
         if: matrix.profile == 'singularity'

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -23,7 +23,7 @@ repos:
       - id: renovate-config-validator
   # use ruff for python files
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.1
+    rev: v0.6.2
     hooks:
       - id: ruff
         files: \.py$

diff --git a/modules/nf-core/atlas/call/meta.yml b/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"

diff --git a/modules/nf-core/atlas/call/tests/main.nf.test b/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()
+				}
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/atlas/call/tests/main.nf.test.snap b/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"
+    }
+}
diff --git a/modules/nf-core/atlas/pmd/meta.yml b/modules/nf-core/atlas/pmd/meta.yml
@@ -11,7 +11,7 @@ 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

diff --git a/modules/nf-core/atlas/pmd/tests/main.nf.test b/modules/nf-core/atlas/pmd/tests/main.nf.test
@@ -0,0 +1,46 @@
+
+nextflow_process {
+
+    name "Test Process ATLAS_PMD"
+    script "../main.nf"
+    process "ATLAS_PMD"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "atlas"
+    tag "atlas/pmd"
+
+    test("test-atlas-pmd") {
+
+        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] = 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)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					file(process.out.empiric[0][1]).readLines()[0],
+					file(process.out.exponential[0][1]).readLines()[0][0..13],
+					file(process.out.counts[0][1]).readLines()[0],
+					file(process.out.table[0][1]).readLines()[0],
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/atlas/pmd/tests/main.nf.test.snap b/modules/nf-core/atlas/pmd/tests/main.nf.test.snap
@@ -0,0 +1,18 @@
+{
+    "test-atlas-pmd": {
+        "content": [
+            "1\tCT\tEmpiric[0.000831,0.000000,0.001339,0.001350,0.001437,0.000000,0.002210,0.001314,0.001466,0.000000,0.001395,0.001403,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.001362,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000794,0.000000,0.000000,0.000000,0.001297,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000]",
+            "1\tExponential[",
+            "1\tforward\tA->A\t2050\t2033\t2081\t2078\t2138\t2119\t2038\t2007\t2035\t2113\t2049\t2048\t1974\t2012\t2066\t2093\t2110\t1971\t1976\t1906\t1968\t1951\t1917\t1912\t1955\t1956\t1933\t1872\t1922\t1933\t1974\t1840\t1963\t1897\t1870\t1823\t1923\t1908\t1902\t1883\t1973\t1899\t1908\t1912\t1972\t1913\t1922\t1959\t1995\t2039",
+            "1\tforward\tA->A\t0.998539\t0.997547\t0.997603\t1\t0.998133\t0.998586\t0.99902\t0.998507\t0.998038\t0.999527\t0.997566\t0.997565\t0.998988\t0.998016\t0.99855\t0.999522\t0.996223\t0.99848\t0.999494\t0.998952\t0.999492\t0.997444\t0.998958\t0.997912\t0.997958\t0.997959\t0.997935\t0.998933\t0.996888\t0.999483\t0.998988\t0.999457\t0.998474\t0.998947\t0.998398\t0.998357\t0.997924\t0.999476\t0.999475\t1\t0.998987\t0.998423\t0.999476\t1\t1\t0.998956\t0.998442\t0.997454\t0.9975\t0.99951",
+            [
+                "versions.yml:md5,abec49256c52cb677fa0dad3473ed5a6"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T16:01:09.837624"
+    }
+}
diff --git a/modules/nf-core/atlas/recal/meta.yml b/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

diff --git a/modules/nf-core/atlas/recal/tests/main.nf.test b/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()
+				}
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/atlas/recal/tests/main.nf.test.snap b/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"
+    }
+}
diff --git a/modules/nf-core/atlas/splitmerge/main.nf b/modules/nf-core/atlas/splitmerge/main.nf
@@ -11,7 +11,8 @@ process ATLAS_SPLITMERGE {
     tuple val(meta), path(bam), path(bai), path(read_group_settings), path(blacklist)
 
     output:
-    tuple val(meta), path("*_mergedReads.bam"), path("*.txt.gz"), emit: data
+    tuple val(meta), path("*_mergedReads.bam")  , emit: bam
+    tuple val(meta), path("*.txt.gz")           , emit: txt
     path "versions.yml", emit: versions
 
     when:

diff --git a/modules/nf-core/atlas/splitmerge/meta.yml b/modules/nf-core/atlas/splitmerge/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
@@ -27,7 +27,7 @@ input:
       type: file
       description: The BAI file for the input BAM file
       pattern: "*.bai"
-  - read_group_setting:
+  - read_group_settings:
       type: file
       description: |
         TXT file containing the split and merge settings for
@@ -55,7 +55,7 @@ output:
       type: file
       description: A BAM file with suffix_mergedReads.bam
       pattern: "*_mergedReads.bam"
-  - filelist:
+  - txt:
       type: file
       description: A file listing all reads that were filtered out in the merging process with suffix_ignoredReads.txt.gz
       pattern: "*.txt.gz"

diff --git a/modules/nf-core/atlas/splitmerge/tests/main.nf.test b/modules/nf-core/atlas/splitmerge/tests/main.nf.test
@@ -0,0 +1,43 @@
+
+nextflow_process {
+
+    name "Test Process ATLAS_SPLITMERGE"
+    script "../main.nf"
+    process "ATLAS_SPLITMERGE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "atlas"
+    tag "atlas/splitmerge"
+
+    test("test-atlas-splitmerge") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ],
+                    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),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/read_group_settings.txt', checkIfExists: true),
+                    []
+                ]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    path(process.out.txt[0][1]).linesGzip[3..7],
+					bam(process.out.bam[0][1]).getReadsMD5(),
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/atlas/splitmerge/tests/main.nf.test.snap b/modules/nf-core/atlas/splitmerge/tests/main.nf.test.snap
@@ -0,0 +1,22 @@
+{
+    "test-atlas-splitmerge": {
+        "content": [
+            [
+                "Read testN:1, rev : not a proper pair (orphan)",
+                "Read testN:99, rev : longer than insert size (TLEN)",
+                "Read testN:99, rev : not a proper pair (orphan)",
+                "Read testN:830, rev : longer than insert size (TLEN)",
+                "Read testN:830, fwd : longer than insert size (TLEN)"
+            ],
+            "66f5f17da47cc4dced99bd17d739b536",
+            [
+                "versions.yml:md5,208f6ef7923cec00ddbcd5825f84a4fa"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T15:33:41.150912"
+    }
+}