Merge branch 'master' into refactor/sentieon

nf-core · Jul 12, 2024 · 872ce8e · 872ce8e
2 parents 2d7d222 + 0554167
commit 872ce8e
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diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
@@ -32,7 +32,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@60edb5dd545a775178f52524783378180af0d1f8 # v4
+      - uses: actions/setup-node@1e60f620b9541d16bece96c5465dc8ee9832be0b # v4
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -30,7 +30,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5
       - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1
         # FIXME Flip this off once we get to less than a couple hundred. Adding
         # this so it will only run against changed files. It'll make it much
@@ -45,7 +45,7 @@ jobs:
         uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
 
       - name: Install NodeJS
-        uses: actions/setup-node@60edb5dd545a775178f52524783378180af0d1f8 # v4
+        uses: actions/setup-node@1e60f620b9541d16bece96c5465dc8ee9832be0b # v4
         with:
           node-version: "20"
 
@@ -60,7 +60,7 @@ jobs:
     steps:
       - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
 
-      - uses: actions/setup-node@60edb5dd545a775178f52524783378180af0d1f8 # v4
+      - uses: actions/setup-node@1e60f620b9541d16bece96c5465dc8ee9832be0b # v4
         with:
           node-version: "20"
 
@@ -151,7 +151,7 @@ jobs:
       - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
 
       - name: Set up Python
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5
         with:
           python-version: "3.11"
 
@@ -197,7 +197,7 @@ jobs:
       - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
 
       - name: Set up Python
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5
         with:
           python-version: "3.11"
 
@@ -413,7 +413,7 @@ jobs:
       - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
 
       - name: Set up Python
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5
         with:
           python-version: "3.11"
 
@@ -664,7 +664,7 @@ jobs:
           mkdir -p $NXF_SINGULARITY_LIBRARYDIR
 
       - name: Set up Python
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5
         with:
           python-version: "3.11"
 

diff --git a/modules/nf-core/barrnap/main.nf b/modules/nf-core/barrnap/main.nf
@@ -32,7 +32,7 @@ process BARRNAP {
         --threads $task.cpus \\
         --kingdom $db \\
         $input \\
-        > rrna_${db}.gff
+        > ${prefix}_${db}.gff
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -44,9 +44,9 @@ process BARRNAP {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-
+    db = dbname ? "${dbname}" : 'bac'
     """
-    touch ${prefix}.gff
+    touch ${prefix}_${db}.gff
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/barrnap/meta.yml b/modules/nf-core/barrnap/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: "https://github.com/tseemann/barrnap"
       documentation: "https://github.com/tseemann/barrnap"
       tool_dev_url: "https://github.com/tseemann/barrnap"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
@@ -23,6 +23,9 @@ input:
       type: file
       description: fastq or fasta file nucleotides (it can be amino acids as well)
       pattern: "*.{fna,fasta,faa,fastq}"
+  - dbname:
+      type: string
+      description: database to use(bacteria, archaea, eukaryota, metazoan mitochondria)
 output:
   - meta:
       type: map

diff --git a/modules/nf-core/barrnap/tests/main.nf.test b/modules/nf-core/barrnap/tests/main.nf.test
@@ -0,0 +1,57 @@
+nextflow_process {
+
+    name "Test Process BARRNAP"
+    script "../main.nf"
+    process "BARRNAP"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "barrnap"
+
+    test("barrnap") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'test', single_end:false ], // meta map
+                                file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
+                                "bac"
+                            ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("barrnap - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'test', single_end:false ], // meta map
+                                file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
+                                "bac"
+                            ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
+
+
diff --git a/modules/nf-core/barrnap/tests/main.nf.test.snap b/modules/nf-core/barrnap/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+    "barrnap - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_bac.gff:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,447eafa60f76f6b84d1c41a2f5c2f76b"
+                ],
+                "gff": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_bac.gff:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,447eafa60f76f6b84d1c41a2f5c2f76b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.1"
+        },
+        "timestamp": "2024-07-10T11:25:35.085998"
+    },
+    "barrnap": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_bac.gff:md5,df19e1b84ba6f691d20c72b397c88abf"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,447eafa60f76f6b84d1c41a2f5c2f76b"
+                ],
+                "gff": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_bac.gff:md5,df19e1b84ba6f691d20c72b397c88abf"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,447eafa60f76f6b84d1c41a2f5c2f76b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.1"
+        },
+        "timestamp": "2024-07-10T11:25:28.621027"
+    }
+}
diff --git a/modules/nf-core/barrnap/tests/tags.yml b/modules/nf-core/barrnap/tests/tags.yml
@@ -0,0 +1,2 @@
+barrnap:
+  - "modules/nf-core/barrnap/**"
diff --git a/modules/nf-core/bcftools/pluginsplit/main.nf b/modules/nf-core/bcftools/pluginsplit/main.nf
@@ -15,8 +15,10 @@ process BCFTOOLS_PLUGINSPLIT {
     path(targets)
 
     output:
-    tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}")  , emit: vcf
-    path "versions.yml"                                 , emit: versions
+    tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf
+    tuple val(meta), path("*.tbi")                    , emit: tbi, optional: true
+    tuple val(meta), path("*.csi")                    , emit: csi, optional: true
+    path "versions.yml"                               , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -32,6 +34,7 @@ process BCFTOOLS_PLUGINSPLIT {
 
     """
     bcftools plugin split \\
+        ${args} \\
         ${vcf} \\
         ${samples_arg} \\
         ${groups_arg} \\
@@ -56,12 +59,17 @@ process BCFTOOLS_PLUGINSPLIT {
                 args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
                 args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
                 "vcf"
-
+    def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" :
+                args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" :
+                args.contains("--write-index") || args.contains("-W") ? "csi" :
+                ""
     def determination_file = samples ?: targets
+    def create_cmd = extension.matches("vcf|bcf") ? "touch " : "echo '' | gzip > "
+    def create_files = "cut -f 3 ${determination_file} | sed -e 's/\$/.${extension}/' > files.txt; while IFS= read -r filename; do ${create_cmd} \"\$filename\"; done < files.txt"
+    def create_index = index.matches("csi|tbi") ? "cut -f 3 ${determination_file} | sed -e 's/\$/.${extension}.${index}/' > indices.txt; touch \$(<indices.txt)" : ""
     """
-    cut -f 3 ${determination_file} | sed -e 's/\$/.${extension}/' > files.txt
-
-    touch \$(<files.txt)
+    ${create_files}
+    ${create_index}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":