Merge branch 'master' into ribodetector

maxibor · web-flow · commit f54b3c001a22 · 2025-10-20T10:29:26.000+02:00
diff --git a/.github/actions/nf-test-action/action.yml b/.github/actions/nf-test-action/action.yml
@@ -30,7 +30,7 @@ runs:
     - name: Set up Python
       uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
       with:
-        python-version: "3.13"
+        python-version: "3.14"
 
     - name: Set up nf-test
       uses: nf-core/setup-nf-test@v1
diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
@@ -11,7 +11,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@3a9db7e6a41a89f618792c92c0e97cc736e1b13f # v10
+      - uses: actions/stale@5f858e3efba33a5ca4407a664cc011ad407f2008 # v10
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an @nf-core/modules contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
           stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an @nf-core/modules contributor. Remove stale label or add a comment if it is still useful."
diff --git a/.github/workflows/close-wishlist.yml b/.github/workflows/close-wishlist.yml
@@ -10,7 +10,7 @@ jobs:
     permissions:
       issues: write
     steps:
-      - uses: actions/stale@3a9db7e6a41a89f618792c92c0e97cc736e1b13f # v10
+      - uses: actions/stale@5f858e3efba33a5ca4407a664cc011ad407f2008 # v10
         with:
           stale-issue-message: "This issue has been tagged as wishlist and no one has assigned themselves to it within a year. It will be closed in 10 days unless someone assigns themselves to it."
           close-issue-message: "This issue was closed because it has been tagged as wishlist and no one worked on it for over a year."
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
@@ -20,7 +20,7 @@ jobs:
 
       # indication that the linting is being fixed
       - name: React on comment
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: eyes
@@ -32,7 +32,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@a0853c24544627f65ddf259abe73b1d18a591444 # v5
+      - uses: actions/setup-node@2028fbc5c25fe9cf00d9f06a71cc4710d4507903 # v6
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php
@@ -52,7 +52,7 @@ jobs:
 
       - name: Post nothing-to-do comment
         if: steps.prettier_status.outputs.result == 'pass'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           issue-number: ${{ github.event.issue.number }}
           body: |
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -132,7 +132,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - uses: actions/cache@0057852bfaa89a56745cba8c7296529d2fc39830 # v4
         id: cache-pip
@@ -180,7 +180,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml
@@ -236,7 +236,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - uses: actions/cache@0057852bfaa89a56745cba8c7296529d2fc39830 # v4
         id: cache-pip-pytest
diff --git a/.github/workflows/reminder.yml b/.github/workflows/reminder.yml
@@ -10,7 +10,7 @@ jobs:
     permissions:
       issues: write
     steps:
-      - uses: actions/stale@3a9db7e6a41a89f618792c92c0e97cc736e1b13f # v10
+      - uses: actions/stale@5f858e3efba33a5ca4407a664cc011ad407f2008 # v10
         with:
           stale-issue-message: "This is a reminder that you assigned yourself to this issue to create a new module / new subworkflow. Please remove yourself from the Assignees if you do not plan to work on this anymore."
           days-before-stale: 178
diff --git a/.github/workflows/update-gpu-snapshot.yml b/.github/workflows/update-gpu-snapshot.yml
@@ -23,7 +23,7 @@ jobs:
     steps:
       # indication that the snapshot is being updated
       - name: React on comment
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: eyes
@@ -38,7 +38,7 @@ jobs:
           echo "test_path=$(echo ${{ github.event.comment.body }} | grep -oP 'path:\s*\K[^ ]+')" >> $GITHUB_OUTPUT
 
       - name: if test path is empty, exit
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         if: steps.get-test-path.outputs.test_path == ''
         with:
           comment-id: ${{ github.event.comment.id }}
@@ -68,7 +68,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - name: Set up nf-test
         uses: nf-core/setup-nf-test@v1
diff --git a/.github/workflows/update-sentieon-snapshot.yml b/.github/workflows/update-sentieon-snapshot.yml
@@ -26,7 +26,7 @@ jobs:
     steps:
       # indication that the snapshot is being updated
       - name: React on comment
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: eyes
@@ -41,7 +41,7 @@ jobs:
           echo "test_path=$(echo ${{ github.event.comment.body }} | grep -oP 'path:\s*\K[^ ]+')" >> $GITHUB_OUTPUT
 
       - name: if test path is empty, exit
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         if: steps.get-test-path.outputs.test_path == ''
         with:
           comment-id: ${{ github.event.comment.id }}
@@ -71,7 +71,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - name: Set up nf-test
         uses: nf-core/setup-nf-test@v1
diff --git a/modules/nf-core/cellranger/mkfastq/main.nf b/modules/nf-core/cellranger/mkfastq/main.nf
@@ -8,12 +8,13 @@ process CELLRANGER_MKFASTQ {
     tuple val(meta), path(csv), path(bcl)
 
     output:
-    tuple val(meta), path("*_outs/outs/fastq_path/**/*.fastq.gz")          , emit: fastq
-    tuple val(meta), path("*_outs/outs/fastq_path/Undetermined*.fastq.gz") , optional:true, emit: undetermined_fastq
-    tuple val(meta), path("*_outs/outs/fastq_path/Reports")                , optional:true, emit: reports
-    tuple val(meta), path("*_outs/outs/fastq_path/Stats")                  , optional:true, emit: stats
-    tuple val(meta), path("*_outs/outs/interop_path/*.bin")                , emit: interop
-    path "versions.yml"                                                    , emit: versions
+    tuple val(meta), path("*_outs/outs/fastq_path/**/**_S[0-9]*_R?_00?.fastq.gz")  , emit: fastq
+    tuple val(meta), path("*_outs/outs/fastq_path/**/**_S[0-9]*_I?_00?.fastq.gz")  , optional:true, emit: fastq_idx
+    tuple val(meta), path("*_outs/outs/fastq_path/Undetermined*.fastq.gz")         , optional:true, emit: undetermined_fastq
+    tuple val(meta), path("*_outs/outs/fastq_path/Reports")                        , optional:true, emit: reports
+    tuple val(meta), path("*_outs/outs/fastq_path/Stats")                          , optional:true, emit: stats
+    tuple val(meta), path("*_outs/outs/interop_path/*.bin")                        , emit: interop
+    path "versions.yml"                                                            , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -58,9 +59,11 @@ process CELLRANGER_MKFASTQ {
     # data for fastq channels
     mkdir -p "${prefix}_outs/outs/fastq_path/sample/files/"
     touch "${prefix}_outs/outs/fastq_path/Undetermined_fake_file.fastq"
-    touch "${prefix}_outs/outs/fastq_path/sample/files/fake_file.fastq"
+    touch "${prefix}_outs/outs/fastq_path/sample/files/fake_sample_S1_R1_001.fastq"
+    touch "${prefix}_outs/outs/fastq_path/sample/files/fake_sample_S1_I1_001.fastq"
     gzip "${prefix}_outs/outs/fastq_path/Undetermined_fake_file.fastq"
-    gzip "${prefix}_outs/outs/fastq_path/sample/files/fake_file.fastq"
+    gzip "${prefix}_outs/outs/fastq_path/sample/files/fake_sample_S1_R1_001.fastq"
+    gzip "${prefix}_outs/outs/fastq_path/sample/files/fake_sample_S1_I1_001.fastq"
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/cellranger/mkfastq/meta.yml b/modules/nf-core/cellranger/mkfastq/meta.yml
@@ -1,6 +1,6 @@
 name: cellranger_mkfastq
-description: Module to create FASTQs needed by the 10x Genomics Cell Ranger tool.
-  Uses the cellranger mkfastq command.
+description: Module to create FASTQs needed by the 10x Genomics Cell Ranger
+  tool. Uses the cellranger mkfastq command.
 keywords:
   - reference
   - mkfastq
@@ -9,9 +9,9 @@ keywords:
   - bcl2fastq
 tools:
   - cellranger:
-      description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process
-        Chromium single-cell data to align reads, generate feature-barcode matrices,
-        perform clustering and other secondary analysis, and more.
+      description: Cell Ranger by 10x Genomics is a set of analysis pipelines that
+        process Chromium single-cell data to align reads, generate feature-barcode
+        matrices, perform clustering and other secondary analysis, and more.
       homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
       documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
       tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
@@ -39,10 +39,20 @@ output:
     - - meta:
           type: map
           description: Groovy Map containing sample information
-      - "*_outs/outs/fastq_path/**/*.fastq.gz":
+      - "*_outs/outs/fastq_path/**/**_S[0-9]*_R?_00?.fastq.gz":
           type: file
-          description: Unaligned FastQ files
-          pattern: "*.fastq.gz"
+          description: Read FastQ files
+          pattern: "*_S[0-9]*_R?_00?.fastq.gz"
+          ontologies:
+            - edam: http://edamontology.org/format_3989 # GZIP format
+  fastq_idx:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information
+      - "*_outs/outs/fastq_path/**/**_S[0-9]*_I?_00?.fastq.gz":
+          type: file
+          description: Index FastQ files
+          pattern: "*_S[0-9]*_I?_00?.fastq.gz"
           ontologies:
             - edam: http://edamontology.org/format_3989 # GZIP format
   undetermined_fastq:
diff --git a/modules/nf-core/cellranger/mkfastq/tests/main.nf.test b/modules/nf-core/cellranger/mkfastq/tests/main.nf.test
@@ -41,6 +41,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     process.out.fastq,
+                    process.out.fastq_idx,
                     process.out.undetermined_fastq,
                     process.out.interop,
                     process.out.versions
@@ -66,6 +67,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     process.out.fastq,
+                    process.out.fastq_idx,
                     process.out.undetermined_fastq,
                     process.out.interop,
                     process.out.versions
@@ -93,6 +95,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     process.out.fastq,
+                    process.out.fastq_idx,
                     process.out.undetermined_fastq,
                     process.out.interop,
                     process.out.versions
diff --git a/modules/nf-core/cellranger/mkfastq/tests/main.nf.test.snap b/modules/nf-core/cellranger/mkfastq/tests/main.nf.test.snap
@@ -8,12 +8,20 @@
                         "lane": 1
                     },
                     [
-                        "test_sample_S1_L001_I1_001.fastq.gz:md5,018b0dbd8daf76fb9f6dfa4729ea0453",
                         "test_sample_S1_L001_R1_001.fastq.gz:md5,df3ddf85d83bd722219c646c7815dbdc",
                         "test_sample_S1_L001_R2_001.fastq.gz:md5,c8a387b517ff5b7e56b85ccbf882efd2"
                     ]
                 ]
             ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "lane": 1
+                    },
+                    "test_sample_S1_L001_I1_001.fastq.gz:md5,018b0dbd8daf76fb9f6dfa4729ea0453"
+                ]
+            ],
             [
                 [
                     {
@@ -41,10 +49,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.8"
         },
-        "timestamp": "2025-04-30T09:38:45.93880441"
+        "timestamp": "2025-10-17T13:59:51.326856635"
     },
     "cellranger - tiny - simple - stub": {
         "content": [
@@ -54,7 +62,16 @@
                         "id": "test",
                         "lane": 1
                     },
-                    "fake_file.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    "fake_sample_S1_R1_001.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "lane": 1
+                    },
+                    "fake_sample_S1_I1_001.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ]
             ],
             [
@@ -80,10 +97,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.8"
         },
-        "timestamp": "2025-04-30T09:43:20.621612663"
+        "timestamp": "2025-10-17T14:03:02.719354675"
     },
     "cellranger - tiny - illumina": {
         "content": [
@@ -94,12 +111,20 @@
                         "lane": 1
                     },
                     [
-                        "test_sample_S1_L001_I1_001.fastq.gz:md5,018b0dbd8daf76fb9f6dfa4729ea0453",
                         "test_sample_S1_L001_R1_001.fastq.gz:md5,df3ddf85d83bd722219c646c7815dbdc",
                         "test_sample_S1_L001_R2_001.fastq.gz:md5,c8a387b517ff5b7e56b85ccbf882efd2"
                     ]
                 ]
             ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "lane": 1
+                    },
+                    "test_sample_S1_L001_I1_001.fastq.gz:md5,018b0dbd8daf76fb9f6dfa4729ea0453"
+                ]
+            ],
             [
                 [
                     {
@@ -127,9 +152,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.8"
         },
-        "timestamp": "2025-04-30T09:41:45.460808866"
+        "timestamp": "2025-10-17T14:01:26.290765021"
     }
 }
diff --git a/modules/nf-core/last/train/main.nf b/modules/nf-core/last/train/main.nf
@@ -34,7 +34,9 @@ process LAST_TRAIN {
 
     echo "id\tsubstitution_percent_identity\tlast -t\tlast -a\tlast -A\tlast -b\tlast -B\tlast -S"         > ${prefix}.train.tsv
     printf "\$(basename ${prefix}.train .target.train)\t"                                                 >> ${prefix}.train.tsv
-    grep 'substitution percent identity' ${prefix}.train | tail -n 1 | awk '{print \$5}' | tr '\\n' '\\t' >> ${prefix}.train.tsv
+    # Do not take the last 'substitution percent identity' value; it is calculated from a matrix rounded to integers
+    grep 'substitution percent identity' ${prefix}.train |
+        tail -n 2 | head -n 1 | awk '{print \$5}'                                        | tr '\\n' '\\t' >> ${prefix}.train.tsv
     grep 'last -t' ${prefix}.train | tail -n 1 | awk '{print \$2}'   | sed -e 's/-t//'   | tr '\\n' '\\t' >> ${prefix}.train.tsv
     grep 'last -a' ${prefix}.train | tail -n 1 | awk '{print \$3}'                       | tr '\\n' '\\t' >> ${prefix}.train.tsv
     grep 'last -A' ${prefix}.train | tail -n 1 | awk '{print \$3}'                       | tr '\\n' '\\t' >> ${prefix}.train.tsv
diff --git a/modules/nf-core/last/train/tests/main.nf.test.snap b/modules/nf-core/last/train/tests/main.nf.test.snap
@@ -70,7 +70,7 @@
                             "id": "contigs",
                             "single_end": false
                         },
-                        "contigs.train.tsv:md5,a2fca4aabda82f0aa481085ce5258886"
+                        "contigs.train.tsv:md5,c8721d9cabf1e2b7c0d2d3dac9ed3db8"
                     ]
                 ],
                 "2": [
@@ -82,7 +82,7 @@
                             "id": "contigs",
                             "single_end": false
                         },
-                        "contigs.train.tsv:md5,a2fca4aabda82f0aa481085ce5258886"
+                        "contigs.train.tsv:md5,c8721d9cabf1e2b7c0d2d3dac9ed3db8"
                     ]
                 ],
                 "param_file": [
@@ -101,8 +101,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nextflow": "25.04.8"
         },
-        "timestamp": "2025-03-10T11:02:48.369194"
+        "timestamp": "2025-10-20T14:56:15.004824885"
     }
 }
