Merge branch 'master' into for_loop_removal

nf-core · Oct 10, 2024 · 0a2da6b · 0a2da6b
2 parents 5d0f0ab + d7462e7
commit 0a2da6b
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Showing 180 changed files with 5,005 additions and 2,222 deletions.
diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
diff --git a/.github/scripts/wave_singularity.py b/.github/scripts/wave_singularity.py
@@ -0,0 +1,54 @@
+#!/usr/bin/env -S uv run
+# /// script
+# requires-python = ">=3.10"
+# dependencies = [
+#     "httpx",
+# ]
+# ///
+
+import logging
+
+import httpx
+
+logger = logging.getLogger(__name__)
+
+image_url = "oras://community.wave.seqera.io/library/pybedtools_bedtools_htslib_pip_pypints:aa20de1f1b5ddb30"
+
+if image_url.startswith("oras://"):
+    image_url = image_url.replace("oras://", "")
+
+wave_api_url = "https://wave.seqera.io"
+url = f"{wave_api_url}/v1alpha1/inspect"
+
+# if platform_pat:
+#     data["toweraccesstoken"] = platform_pat
+# else:
+# TODO
+logger.warning("'platform_pat' not set, no auth to wave back end")
+
+try:
+    logger.info(f"calling image inspect at {url} for image url {image_url}")
+    response = httpx.post(
+        url=url,
+        json={"containerImage": image_url},
+        headers={"content-type": "application/json"},
+    )
+
+    data = response.json()
+    logger.debug(data)
+    layers = data.get("container", {}).get("manifest", {}).get("layers", [])
+    is_singularity = len(layers) == 1 and layers[0].get("mediaType", "").endswith(".sif")
+    if not is_singularity:
+        print(layers)
+        raise ValueError("not a singularity image")
+    if "digest" not in layers[0]:
+        print(layers)
+        raise ValueError("no 'digest' in first layer found")
+
+    digest = layers[0]["digest"].replace("sha256:", "")
+    container_url = f"https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/{digest[:2]}/{digest}/data"
+    print(container_url)
+
+except httpx.RequestError as exc:
+    print(f"An error occurred while requesting {exc.request.url!r}.")
+    print("No singularity image for you")
diff --git a/.github/workflows/fix-linting.yml b/.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@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -29,7 +29,7 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
       - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # 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@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
 
       - name: Install NodeJS
         uses: actions/setup-node@0a44ba7841725637a19e28fa30b79a866c81b0a6 # v4
@@ -58,7 +58,7 @@ jobs:
   editorconfig:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
 
       - uses: actions/setup-node@0a44ba7841725637a19e28fa30b79a866c81b0a6 # v4
         with:
@@ -78,7 +78,7 @@ jobs:
       modules: ${{ steps.tags.outputs.modules }}
       subworkflows: ${{ steps.tags.outputs.subworkflows }}
     steps:
-      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
         with:
           fetch-depth: 2 # To retrieve the preceding commit.
 
@@ -111,7 +111,7 @@ jobs:
       # Prod for version bumping
 
     steps:
-      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
         with:
           fetch-depth: 0
 
@@ -148,14 +148,14 @@ jobs:
             "${{ fromJson(needs.nf-test-changes.outputs.modules) }}",
           ]
     steps:
-      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
 
       - name: Set up Python
         uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
         with:
           python-version: "3.11"
 
-      - uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
+      - uses: actions/cache@3624ceb22c1c5a301c8db4169662070a689d9ea8 # v4
         id: cache-pip
         with:
           path: ~/.cache/pip
@@ -194,7 +194,7 @@ jobs:
             "${{ fromJson(needs.nf-test-changes.outputs.subworkflows) }}",
           ]
     steps:
-      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
 
       - name: Set up Python
         uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
@@ -398,14 +398,14 @@ jobs:
       NXF_ANSI_LOG: false
 
     steps:
-      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
 
       - name: Set up Python
         uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
         with:
           python-version: "3.11"
 
-      - uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
+      - uses: actions/cache@3624ceb22c1c5a301c8db4169662070a689d9ea8 # v4
         id: cache-pip-pytest
         with:
           path: ~/.cache/pip
@@ -472,7 +472,7 @@ jobs:
 
       - name: Upload logs on failure
         if: failure()
-        uses: actions/upload-artifact@50769540e7f4bd5e21e526ee35c689e35e0d6874 # v4
+        uses: actions/upload-artifact@604373da6381bf24206979c74d06a550515601b9 # v4
         with:
           name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }}
           path: |
@@ -653,7 +653,7 @@ jobs:
       SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }}
 
     steps:
-      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
 
       - uses: actions/setup-java@b36c23c0d998641eff861008f374ee103c25ac73 # v4
         with:
@@ -682,7 +682,7 @@ jobs:
         with:
           python-version: "3.11"
 
-      - uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
+      - uses: actions/cache@3624ceb22c1c5a301c8db4169662070a689d9ea8 # v4
         id: cache-pip-pdiff
         with:
           path: ~/.cache/pip

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -6,7 +6,7 @@ repos:
         additional_dependencies:
           - [email protected]
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.29.2
+    rev: 0.29.3
     hooks:
       - id: check-jsonschema
         # match meta.ymls in one of the subdirectories of modules/nf-core

diff --git a/modules/nf-core/bamtofastq10x/main.nf b/modules/nf-core/bamtofastq10x/main.nf
@@ -11,8 +11,8 @@ process BAMTOFASTQ10X {
     tuple val(meta), path(bam)
 
     output:
-    tuple val(meta), path("*.fastq.gz"), emit: fastq
-    path "versions.yml"                , emit: versions
+    tuple val(meta), path("**/*.fastq.gz"), emit: fastq
+    path "versions.yml"                   , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -24,7 +24,7 @@ process BAMTOFASTQ10X {
     bamtofastq \\
         $args \\
         $bam \\
-        ${prefix}.fastq.gz
+        $prefix
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -35,7 +35,8 @@ process BAMTOFASTQ10X {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.fastq.gz
+    mkdir -p ${prefix}/bamtofastq10x
+    touch ${prefix}/bamtofastq10x/bamtofastq.fastq.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/bamtofastq10x/meta.yml b/modules/nf-core/bamtofastq10x/meta.yml
@@ -37,10 +37,10 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1', single_end:false ]`
-      - "*.fastq.gz":
+      - "**/*.fastq.gz":
           type: file
           description: fastq compressed file
-          pattern: "*.fastq.gz"
+          pattern: "**/*.fastq.gz"
   - versions:
       - versions.yml:
           type: file

diff --git a/modules/nf-core/bamtofastq10x/tests/main.nf.test.snap b/modules/nf-core/bamtofastq10x/tests/main.nf.test.snap
@@ -8,11 +8,9 @@
                             "id": "test"
                         },
                         [
-                            [
-                                "bamtofastq_S1_L000_I1_001.fastq.gz:md5,a33682ac881de7a7453d79721b7621a0",
-                                "bamtofastq_S1_L000_R1_001.fastq.gz:md5,5ccebf77d8636d7a7cdfc59737aea79f",
-                                "bamtofastq_S1_L000_R2_001.fastq.gz:md5,2ee7c90e4307deba74065cfd00a65002"
-                            ]
+                            "bamtofastq_S1_L000_I1_001.fastq.gz:md5,a33682ac881de7a7453d79721b7621a0",
+                            "bamtofastq_S1_L000_R1_001.fastq.gz:md5,5ccebf77d8636d7a7cdfc59737aea79f",
+                            "bamtofastq_S1_L000_R2_001.fastq.gz:md5,2ee7c90e4307deba74065cfd00a65002"
                         ]
                     ]
                 ],
@@ -25,11 +23,9 @@
                             "id": "test"
                         },
                         [
-                            [
-                                "bamtofastq_S1_L000_I1_001.fastq.gz:md5,a33682ac881de7a7453d79721b7621a0",
-                                "bamtofastq_S1_L000_R1_001.fastq.gz:md5,5ccebf77d8636d7a7cdfc59737aea79f",
-                                "bamtofastq_S1_L000_R2_001.fastq.gz:md5,2ee7c90e4307deba74065cfd00a65002"
-                            ]
+                            "bamtofastq_S1_L000_I1_001.fastq.gz:md5,a33682ac881de7a7453d79721b7621a0",
+                            "bamtofastq_S1_L000_R1_001.fastq.gz:md5,5ccebf77d8636d7a7cdfc59737aea79f",
+                            "bamtofastq_S1_L000_R2_001.fastq.gz:md5,2ee7c90e4307deba74065cfd00a65002"
                         ]
                     ]
                 ],
@@ -39,9 +35,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-22T16:43:24.999397"
+        "timestamp": "2024-10-02T12:56:21.808042"
     }
 }
diff --git a/modules/nf-core/bcftools/filter/main.nf b/modules/nf-core/bcftools/filter/main.nf
@@ -8,7 +8,7 @@ process BCFTOOLS_FILTER {
         'biocontainers/bcftools:1.20--h8b25389_0' }"
 
     input:
-    tuple val(meta), path(vcf)
+    tuple val(meta), path(vcf), path(tbi)
 
     output:
     tuple val(meta), path("*.${extension}"), emit: vcf

diff --git a/modules/nf-core/bcftools/filter/meta.yml b/modules/nf-core/bcftools/filter/meta.yml
@@ -23,6 +23,10 @@ input:
         type: file
         description: VCF input file
         pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}"
+    - tbi:
+        type: file
+        description: VCF index file
+        pattern: "*.tbi"
 output:
   - vcf:
       - meta: