Fix/prevent falco module to process an empty fastq file

.devcontainer/devcontainer.json

@@ -18,7 +18,7 @@
         }
     },
     "features": {
-        "ghcr.io/devcontainers/features/github-cli:1": {},
-        "ghcr.io/devcontainers/features/docker-in-docker:2.9": {}
+        "ghcr.io/devcontainers/features/github-cli:1@sha256:464564228ccdd6028f01f8a62a3cfbaf76e9ba7953b29ac0e53ba2c262604312": {},
+        "ghcr.io/devcontainers/features/docker-in-docker:2.9@sha256:9074d8eaf4585ab1498c81a8762078992725614fc7a9cfafe799aa22717a6bbf": {}
     }
 }

.github/workflows/fix-linting.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 

.github/workflows/test.yml

@@ -29,7 +29,7 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
       - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
       - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1
         # FIXME Flip this off once we get to less than a couple hundred. Adding
@@ -42,7 +42,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
 
       - name: Install NodeJS
         uses: actions/setup-node@60edb5dd545a775178f52524783378180af0d1f8 # v4
@@ -58,7 +58,7 @@ jobs:
   editorconfig:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
 
       - uses: actions/setup-node@60edb5dd545a775178f52524783378180af0d1f8 # v4
         with:
@@ -78,7 +78,7 @@ jobs:
       modules: ${{ steps.tags.outputs.modules }}
       subworkflows: ${{ steps.tags.outputs.subworkflows }}
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
         with:
           fetch-depth: 2 # To retrieve the preceding commit.
 
@@ -111,7 +111,7 @@ jobs:
       # Prod for version bumping
 
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
         with:
           fetch-depth: 0
 
@@ -148,7 +148,7 @@ jobs:
             "${{ fromJson(needs.nf-test-changes.outputs.modules) }}",
           ]
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
 
       - name: Set up Python
         uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
@@ -194,7 +194,7 @@ jobs:
             "${{ fromJson(needs.nf-test-changes.outputs.subworkflows) }}",
           ]
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
 
       - name: Set up Python
         uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
@@ -411,7 +411,7 @@ jobs:
       SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
 
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
 
       - name: Set up Python
         uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
@@ -649,7 +649,7 @@ jobs:
       NFTEST_VER: "0.8.4"
 
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
 
       - uses: actions/setup-java@99b8673ff64fbf99d8d325f52d9a5bdedb8483e9 # v4
         with:

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ repos:
         additional_dependencies:
           - prettier@3.2.5
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.28.3
+    rev: 0.28.4
     hooks:
       - id: check-jsonschema
         # match meta.ymls in one of the subdirectories of modules/nf-core
@@ -18,12 +18,12 @@ repos:
         args: ["--schemafile", "subworkflows/yaml-schema.json"]
       - id: check-github-workflows
   - repo: https://github.com/renovatebot/pre-commit-hooks
-    rev: 37.356.1
+    rev: 37.382.4
     hooks:
       - id: renovate-config-validator
   # use ruff for python files
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.3
+    rev: v0.4.6
     hooks:
       - id: ruff
         files: \.py$

modules/nf-core/annotsv/annotsv/environment.yml

@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::annotsv=3.4.1
+  - bioconda::annotsv=3.4.2

modules/nf-core/annotsv/annotsv/main.nf

@@ -4,8 +4,8 @@ process ANNOTSV_ANNOTSV {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/annotsv:3.4.1--py312hdfd78af_1' :
-        'biocontainers/annotsv:3.4.1--py312hdfd78af_1' }"
+        'oras://community.wave.seqera.io/library/annotsv:3.4.2--141a0ee560de1897' :
+        'community.wave.seqera.io/library/annotsv:3.4.2--010fa21247b5b64b' }"
 
     input:
     tuple val(meta), path(sv_vcf), path(sv_vcf_index), path(candidate_small_variants)

modules/nf-core/annotsv/annotsv/tests/main.nf.test.snap

@@ -25,7 +25,7 @@
 
                 ],
                 "3": [
-                    "versions.yml:md5,4fc0e1da7e278fb8b421d8c1af873e68"
+                    "versions.yml:md5,a5c7d9d19db00a62006faa1bafa917ec"
                 ],
                 "tsv": [
                     [
@@ -50,14 +50,14 @@
 
                 ],
                 "versions": [
-                    "versions.yml:md5,4fc0e1da7e278fb8b421d8c1af873e68"
+                    "versions.yml:md5,a5c7d9d19db00a62006faa1bafa917ec"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.03.0"
+            "nextflow": "24.04.1"
         },
-        "timestamp": "2024-05-07T09:49:40.626698361"
+        "timestamp": "2024-05-29T15:10:39.33144868"
     }
 }

modules/nf-core/annotsv/installannotations/environment.yml

@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::annotsv=3.4.1
+  - bioconda::annotsv=3.4.2

modules/nf-core/annotsv/installannotations/main.nf

@@ -4,8 +4,8 @@ process ANNOTSV_INSTALLANNOTATIONS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/annotsv:3.4.1--py312hdfd78af_1' :
-        'biocontainers/annotsv:3.4.1--py312hdfd78af_1' }"
+        'oras://community.wave.seqera.io/library/annotsv:3.4.2--141a0ee560de1897' :
+        'community.wave.seqera.io/library/annotsv:3.4.2--010fa21247b5b64b' }"
 
     output:
     path "AnnotSV_annotations", emit: annotations

modules/nf-core/annotsv/installannotations/tests/main.nf.test

@@ -9,20 +9,6 @@ nextflow_process {
     tag "annotsv"
     tag "annotsv/installannotations"
 
-    test("homo_sapiens") {
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(
-                    process.out.annotations.collect { file(it).name },
-                    process.out.versions
-                ).match() }
-            )
-        }
-
-    }
-
     test("homo_sapiens - stub") {
 
         options "-stub"

modules/nf-core/annotsv/installannotations/tests/main.nf.test.snap

@@ -8,37 +8,22 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,81e3dc46efd769339d47ef9eb1775cba"
+                    "versions.yml:md5,d0b3dc5e0199653fd81ffd3754e65f9c"
                 ],
                 "annotations": [
                     [
                         "stub_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,81e3dc46efd769339d47ef9eb1775cba"
+                    "versions.yml:md5,d0b3dc5e0199653fd81ffd3754e65f9c"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.03.0"
+            "nextflow": "24.04.1"
         },
-        "timestamp": "2024-05-07T15:55:34.32067216"
-    },
-    "homo_sapiens": {
-        "content": [
-            [
-                "AnnotSV_annotations"
-            ],
-            [
-                "versions.yml:md5,81e3dc46efd769339d47ef9eb1775cba"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.03.0"
-        },
-        "timestamp": "2024-05-07T14:16:29.103169977"
+        "timestamp": "2024-05-29T15:14:54.723053976"
     }
 }

modules/nf-core/antismash/antismashlite/main.nf

@@ -57,6 +57,7 @@ process ANTISMASH_ANTISMASHLITE {
         $gff_flag \\
         -c $task.cpus \\
         --output-dir $prefix \\
+        --output-basename $prefix \\
         --genefinding-tool none \\
         --logfile $prefix/${prefix}.log \\
         --databases $databases \\

modules/nf-core/bamcmp/tests/main.nf.test.snap

@@ -7,15 +7,15 @@
                         {
                             "id": "test"
                         },
-                        "test_primary.bam:md5,1a1b5fbca218a8b31858a93b87170c84"
+                        "test_primary.bam:md5,98279f796da12feb21649065b4829966"
                     ]
                 ],
                 "1": [
                     [
                         {
                             "id": "test"
                         },
-                        "test_contaminant.bam:md5,a3463b6aa464675fb575fca5f292d459"
+                        "test_contaminant.bam:md5,82fc64a47109d9ee87d9de71e5bcbf2a"
                     ]
                 ],
                 "2": [
@@ -26,15 +26,15 @@
                         {
                             "id": "test"
                         },
-                        "test_contaminant.bam:md5,a3463b6aa464675fb575fca5f292d459"
+                        "test_contaminant.bam:md5,82fc64a47109d9ee87d9de71e5bcbf2a"
                     ]
                 ],
                 "primary_filtered_bam": [
                     [
                         {
                             "id": "test"
                         },
-                        "test_primary.bam:md5,1a1b5fbca218a8b31858a93b87170c84"
+                        "test_primary.bam:md5,98279f796da12feb21649065b4829966"
                     ]
                 ],
                 "versions": [
@@ -46,7 +46,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-04-09T13:21:03.481279358"
+        "timestamp": "2024-05-20T08:44:10.44755427"
     },
     "bamcmp - stub": {
         "content": [

modules/nf-core/bamtofastq10x/environment.yml

@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "bamtofastq10x"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::10x_bamtofastq=1.4.1"

modules/nf-core/bamtofastq10x/main.nf

@@ -0,0 +1,45 @@
+process BAMTOFASTQ10X {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/10x_bamtofastq:1.4.1--hdbdd923_2':
+        'biocontainers/10x_bamtofastq:1.4.1--hdbdd923_2' }"
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("*.fastq.gz"), emit: fastq
+    path "versions.yml"                , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    bamtofastq \\
+        $args \\
+        $bam \\
+        ${prefix}.fastq.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bamtofastq10x: \$(bamtofastq --version |& sed '1!d ; s/bamtofastq //')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.fastq.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bamtofastq10x: \$(bamtofastq --version |& sed '1!d ; s/bamtofastq //')
+    END_VERSIONS
+    """
+}