Merge remote-tracking branch 'upstream/master'

Author: sainsachiko

.devcontainer/devcontainer.json

@@ -1,28 +1,20 @@
 {
-    "name": "nfcore",
-    "image": "nfcore/gitpod:dev",
-    "remoteUser": "gitpod",
-    "runArgs": ["--privileged"],
-    // Configure tool-specific properties.
-    "customizations": {
-        // Configure properties specific to VS Code.
-        "vscode": {
-            // Set *default* container specific settings.json values on container create.
-            "settings": {
-                "python.defaultInterpreterPath": "/opt/conda/bin/python",
-                "python.linting.enabled": true
-            },
+    "name": "nfcore-modules",
+    "image": "nfcore/devcontainer:dev",
 
-            // Add the IDs of extensions you want installed when the container is created.
-            "extensions": ["nf-core.nf-core-extensionpack"]
-        }
+    "remoteEnv": {
+        // Workspace path on the host for mounting with docker-outside-of-docker
+        "LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
     },
-    "features": {
-        "ghcr.io/devcontainers/features/github-cli:1.0.11": {
-            "digest": "sha256:464564228ccdd6028f01f8a62a3cfbaf76e9ba7953b29ac0e53ba2c262604312"
-        },
-        "ghcr.io/devcontainers/features/docker-in-docker:2.9.2": {
-            "digest": "sha256:9074d8eaf4585ab1498c81a8762078992725614fc7a9cfafe799aa22717a6bbf"
-        }
+
+    "onCreateCommand": "./.devcontainer/setup.sh",
+
+    "remoteUser": "root",
+    "privileged": true,
+
+    "hostRequirements": {
+        "cpus": 4,
+        "memory": "16gb",
+        "storage": "32gb"
     }
 }

.devcontainer/setup.sh

@@ -0,0 +1,16 @@
+#!/usr/bin/env bash
+
+# Customise the terminal command prompt
+echo "export PROMPT_DIRTRIM=2" >> $HOME/.bashrc
+echo "export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '" >> $HOME/.bashrc
+export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
+
+# Update Nextflow
+nextflow self-update
+
+# Install prek hooks
+pip install prek
+prek install --install-hooks
+
+# Update welcome message
+echo "Welcome to nf-core/modules devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt

.editorconfig

@@ -1,20 +1,31 @@
-.github/workflows/** @nf-core/a-team
-tests/config @nf-core/a-team
+# Everything is OWNED by infrastructure and ops
+* @nf-core/infrastructure @nf-core/ops
+# Except for modules and subworkflows
+modules
+subworkflows
 
-# Opt-in
-modules/nf-core/bedtools/** @edmundmiller
-modules/nf-core/dragmap/** @edmundmiller
-modules/nf-core/ensemblvep/** @maxulysse
-modules/nf-core/gatk4/** @maxulysse
-modules/nf-core/homer/** @edmundmiller
-modules/nf-core/snpeff/** @maxulysse
-modules/nf-core/pints/caller/** @edmundmiller
-modules/nf-core/preseq/ccurve/** @edmundmiller
-modules/nf-core/preseq/lcextrap/** @edmundmiller
-subworkflows/nf-core/homer/** @edmundmiller
-modules/nf-core/**/Dockerfile @edmundmiller @maxulysse
-subworkflows/nf-core/abundance_differential_filter/** @pinin4fjords
-subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/** @pinin4fjords
+# Opt-in for specific modules, subworkflows or files
+Dockerfile @edmundmiller @maxulysse
+modules/nf-core/bwa/index @maxulysse
+modules/nf-core/bwa/mem @maxulysse
+modules/nf-core/bwamem2 @maxulysse
+modules/nf-core/bedtools @edmundmiller
 modules/nf-core/deseq2 @pinin4fjords
+modules/nf-core/dragmap @edmundmiller
+modules/nf-core/ensemblvep @maxulysse
+modules/nf-core/gatk4 @maxulysse
+modules/nf-core/gatk4spark @maxulysse
+modules/nf-core/homer @edmundmiller
 modules/nf-core/limma @pinin4fjords
+modules/nf-core/pints/caller @edmundmiller
+modules/nf-core/preseq/ccurve @edmundmiller
+modules/nf-core/preseq/lcextrap @edmundmiller
 modules/nf-core/shinyngs @pinin4fjords
+modules/nf-core/snpeff @maxulysse
+subworkflows/nf-core/archive_extract @maxulysse
+subworkflows/nf-core/abundance_differential_filter @pinin4fjords
+subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness @pinin4fjords
+subworkflows/nf-core/homer @edmundmiller
+subworkflows/nf-core/vcf_annotate_ensemblvep @maxulysse
+subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff @maxulysse
+subworkflows/nf-core/vcf_annotate_snpeff @maxulysse

.github/CODEOWNERS

@@ -17,7 +17,7 @@ inputs:
 runs:
   using: "composite"
   steps:
-    - uses: actions/setup-java@c5195efecf7bdfc987ee8bae7a71cb8b11521c00 # v4
+    - uses: actions/setup-java@dded0888837ed1f317902acf8a20df0ad188d165 # v5
       with:
         distribution: "temurin"
         java-version: "17"
@@ -28,9 +28,9 @@ runs:
         version: "${{ env.NXF_VERSION }}"
 
     - name: Set up Python
-      uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      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

.github/actions/nf-test-action/action.yml

@@ -2,14 +2,25 @@
     $schema: "https://docs.renovatebot.com/renovate-schema.json",
     extends: [
         "github>nf-core/ops//.github/renovate/default.json5",
-        "github>nf-core/ops//.github/renovate/process_updaters.json5",
+        // "github>nf-core/ops//.github/renovate/process_updaters.json5",
     ],
     prHeader: "## WARNING\n - [ ] I have made sure to update the singularity and conda images",
     packageRules: [
         {
             matchDatasources: ["conda", "pypi", "docker"],
             automerge: false,
         },
+        {
+            matchManagers: [
+                "github-actions",
+                "npm",
+                "pip_requirements",
+                "pip_setup",
+            ],
+            groupName: "Infrastructural dependencies",
+            schedule: ["before 6am on Monday"],
+            matchPackageNames: ["!/biocontainers/*/"],
+        },
     ],
     customManagers: [
         {

.github/renovate.json5

@@ -2,13 +2,13 @@
     "conda": [
         "modules/nf-core/angsd/gl",
         "modules/nf-core/annotsv/installannotations",
-        "modules/nf-core/backsub",
         "modules/nf-core/bakta/bakta",
         "modules/nf-core/bakta/baktadbdownload",
         "modules/nf-core/bases2fastq",
         "modules/nf-core/basicpy",
         "modules/nf-core/bcl2fastq",
         "modules/nf-core/bclconvert",
+        "modules/nf-core/braker3",
         "modules/nf-core/celesta",
         "modules/nf-core/cellpose",
         "modules/nf-core/cellranger/count",
@@ -18,15 +18,17 @@
         "modules/nf-core/cellranger/mkvdjref",
         "modules/nf-core/cellranger/multi",
         "modules/nf-core/cellranger/vdj",
-        "modules/nf-core/cellrangerarc/mkref",
         "modules/nf-core/cellrangerarc/count",
-        "modules/nf-core/cellrangerarc/mkgtf",
         "modules/nf-core/cellrangerarc/mkfastq",
+        "modules/nf-core/cellrangerarc/mkgtf",
+        "modules/nf-core/cellrangerarc/mkref",
+        "modules/nf-core/cellrangeratac/count",
         "modules/nf-core/cellrangeratac/mkfastq",
         "modules/nf-core/cellrangeratac/mkref",
-        "modules/nf-core/cellrangeratac/count",
         "modules/nf-core/checkqc",
         "modules/nf-core/coreograph",
+        "modules/nf-core/ctatsplicing/prepgenomelib",
+        "modules/nf-core/ctatsplicing/startocancerintrons",
         "modules/nf-core/custom/dumpsoftwareversions",
         "modules/nf-core/deepcell/mesmer",
         "modules/nf-core/deepsomatic",
@@ -36,12 +38,16 @@
         "modules/nf-core/deepvariant/postprocessvariants",
         "modules/nf-core/deepvariant/rundeepvariant",
         "modules/nf-core/deepvariant/vcfstatsreport",
+        "subworkflows/nf-core/dia_proteomics_analysis",
+        "modules/nf-core/diann",
         "modules/nf-core/doubletdetection",
         "modules/nf-core/fastk/fastk",
         "modules/nf-core/fastk/histex",
         "modules/nf-core/fastk/merge",
         "modules/nf-core/fcs/fcsadaptor",
         "modules/nf-core/fcs/fcsgx",
+        "modules/nf-core/force/cube",
+        "modules/nf-core/force/tileextent",
         "modules/nf-core/ganon/buildcustom",
         "modules/nf-core/ganon/classify",
         "modules/nf-core/ganon/report",
@@ -62,16 +68,15 @@
         "modules/nf-core/merquryfk/katgc",
         "modules/nf-core/merquryfk/merquryfk",
         "modules/nf-core/merquryfk/ploidyplot",
-        "modules/nf-core/mitohifi/mitohifi",
         "modules/nf-core/mitohifi/findmitoreference",
+        "modules/nf-core/mitohifi/mitohifi",
         "modules/nf-core/molkartgarage/clahe",
         "modules/nf-core/ncbitools/vecscreen",
         "modules/nf-core/parabricks",
-        "modules/nf-core/purgedups/histplot",
         "modules/nf-core/purgedups/calcuts",
         "modules/nf-core/purgedups/getseqs",
+        "modules/nf-core/purgedups/histplot",
         "modules/nf-core/purgedups/purgedups",
-        "modules/nf-core/quartonotebook",
         "modules/nf-core/scimap/mcmicro",
         "modules/nf-core/scimap/spatiallda",
         "modules/nf-core/sentieon/bwaindex",
@@ -94,19 +99,27 @@
         "modules/nf-core/xeniumranger/relabel",
         "modules/nf-core/xeniumranger/rename",
         "modules/nf-core/xeniumranger/resegment",
+        "modules/nf-core/opt/flip",
+        "modules/nf-core/opt/track",
+        "modules/nf-core/opt/stat",
+        "subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_strelka",
         "subworkflows/nf-core/bcl_demultiplex",
         "subworkflows/nf-core/deepvariant",
         "subworkflows/nf-core/fasta_clean_fcs",
         "subworkflows/nf-core/fasta_newick_epang_gappa",
         "subworkflows/nf-core/fastq_align_bamcmp_bwa",
         "subworkflows/nf-core/fastq_align_bwa"
     ],
-    "docker": ["modules/nf-core/parabricks", "subworkflows/nf-core/deepvariant/tests/equality"],
+    "docker": [
+        "modules/nf-core/parabricks",
+        "modules/nf-core/sparsesignatures",
+        "subworkflows/nf-core/deepvariant/tests/equality"
+    ],
     "singularity": [
         "modules/nf-core/bases2fastq",
+        "modules/nf-core/deepsomatic",
         "modules/nf-core/deepvariant/rundeepvariant",
         "modules/nf-core/deepvariant/vcfstatsreport",
-        "modules/nf-core/deepsomatic",
         "modules/nf-core/parabricks",
         "modules/nf-core/universc",
         "subworkflows/nf-core/deepvariant/tests/equality"

.github/skip_nf_test.json

@@ -11,7 +11,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@5bef64f19d7facfb25b37b414482c7164d639639 # v9
+      - 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."

.github/workflows/clean-up.yml

@@ -0,0 +1,19 @@
+name: "Close wishlist issues"
+on:
+  schedule:
+    - cron: "0 0 * * 0" # Once a week
+  workflow_dispatch:
+
+jobs:
+  clean-up:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+    steps:
+      - 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."
+          days-before-stale: 346
+          days-before-close: 10
+          any-of-labels: "wishlist"

.github/workflows/close-wishlist.yml

@@ -14,13 +14,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
       # 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
@@ -32,35 +32,22 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020 # v4
-
-      - name: Install Prettier
-        run: npm install -g prettier @prettier/plugin-php
-
-      # Check that we actually need to fix something
-      - name: Run 'prettier --check'
-        id: prettier_status
-        run: |
-          if prettier --check ${GITHUB_WORKSPACE}; then
-            echo "::set-output name=result::pass"
-          else
-            echo "::set-output name=result::fail"
-          fi
-      - name: Run 'prettier --write'
-        if: steps.prettier_status.outputs.result == 'fail'
-        run: prettier --write ${GITHUB_WORKSPACE}
+      - name: Run prek
+        id: prek
+        uses: j178/prek-action@v1
+        continue-on-error: true
 
       - name: Post nothing-to-do comment
-        if: steps.prettier_status.outputs.result == 'pass'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        if: steps.prek.outcome == 'success'
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           issue-number: ${{ github.event.issue.number }}
           body: |
             Nothing for me to do here! :shrug:
             This is probably because the linting errors come from `nf-core lint` and have to be fixed manually (or with `nf-core lint --fix`).
 
       - name: Commit & push changes
-        if: steps.prettier_status.outputs.result == 'fail'
+        if: steps.prek.outcome == 'failure'
         run: |
           git config user.email "[email protected]"
           git config user.name "nf-core-bot"