Release v1.1.0

.devcontainer/devcontainer.json

@@ -1,20 +1,21 @@
 {
+    "$schema": "https://raw.githubusercontent.com/devcontainers/spec/main/schemas/devContainer.schema.json",
     "name": "nfcore",
-    "image": "nfcore/gitpod:latest",
-    "remoteUser": "gitpod",
-    "runArgs": ["--privileged"],
+    "image": "nfcore/devcontainer:latest",
 
-    // 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"
-            },
+    "remoteUser": "root",
+    "privileged": true,
 
-            // Add the IDs of extensions you want installed when the container is created.
-            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
-        }
+    "remoteEnv": {
+        // Workspace path on the host for mounting with docker-outside-of-docker
+        "LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
+    },
+
+    "onCreateCommand": "./.devcontainer/setup.sh",
+
+    "hostRequirements": {
+        "cpus": 4,
+        "memory": "16gb",
+        "storage": "32gb"
     }
 }

.devcontainer/setup.sh

@@ -0,0 +1,13 @@
+#!/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 PROMPT_DIRTRIM=2
+export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
+
+# Update Nextflow
+nextflow self-update
+
+# Update welcome message
+echo "Welcome to the nf-cmgg/report devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt

.gitattributes

@@ -2,3 +2,5 @@
 *.nf.test linguist-language=nextflow
 modules/nf-core/** linguist-generated
 subworkflows/nf-core/** linguist-generated
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,7 @@
+contact_links:
+  - name: Join nf-core
+    url: https://nf-co.re/join
+    about: Please join the nf-core community here
+  - name: "Slack #report channel"
+    url: https://nfcore.slack.com/channels/report
+    about: Discussion about the nf-cmgg/report pipeline

.github/PULL_REQUEST_TEMPLATE.md

@@ -8,14 +8,14 @@ These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-cmgg/report/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-cmgg/report/tree/master/docs/CONTRIBUTING.md)
 -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-cmgg/report/tree/master/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-cmgg/report/tree/master/docs/CONTRIBUTING.md)
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).

.github/actions/get-shards/action.yml

@@ -7,6 +7,9 @@ inputs:
   paths:
     description: "Component paths to test"
     required: false
+  tags:
+    description: "Tags to pass as argument for nf-test --tag parameter"
+    required: false
 outputs:
   shard:
     description: "Array of shard numbers"
@@ -18,7 +21,7 @@ runs:
   using: "composite"
   steps:
     - name: Install nf-test
-      uses: nf-core/setup-nf-test@v1
+      uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2
       with:
         version: ${{ env.NFT_VER }}
     - name: Get number of shards
@@ -27,8 +30,9 @@ runs:
       run: |
         # Run nf-test with dynamic parameter
         nftest_output=$(nf-test test \
-          --dry-run \
           --profile +docker \
+          $(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \
+          --dry-run \
           --ci \
           --changed-since HEAD^) || {
             echo "nf-test command failed with exit code $?"

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

@@ -13,28 +13,31 @@ inputs:
   paths:
     description: "Test paths"
     required: true
-
+  tags:
+    description: "Tags to pass as argument for nf-test --tag parameter"
+    required: false
 runs:
   using: "composite"
   steps:
     - name: Setup Nextflow
-      uses: nf-core/setup-nextflow@v2
+      uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
       with:
         version: "${{ env.NXF_VERSION }}"
 
     - name: Set up Python
-      uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
+      uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
       with:
-        python-version: "3.11"
+        python-version: "3.14"
 
     - name: Install nf-test
-      uses: nf-core/setup-nf-test@v1
+      uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2
       with:
         version: "${{ env.NFT_VER }}"
+        install-pdiff: true
 
     - name: Setup apptainer
       if: contains(inputs.profile, 'singularity')
-      uses: eWaterCycle/setup-apptainer@main
+      uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2
 
     - name: Set up Singularity
       if: contains(inputs.profile, 'singularity')
@@ -43,37 +46,18 @@ runs:
         mkdir -p $NXF_SINGULARITY_CACHEDIR
         mkdir -p $NXF_SINGULARITY_LIBRARYDIR
 
-    - name: Conda setup
-      if: ${{inputs.profile == 'conda'}}
-      uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3
-      with:
-        auto-update-conda: true
-        conda-solver: libmamba
-        conda-remove-defaults: true
-
-    - name: Install pdiff
-      shell: bash
-      run: |
-        python -m pip install pdiff
-
-    - name: Clean up Disk space
-      uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
-
-      # TODO Skip failing conda tests and document their failures
-      # https://github.com/nf-core/modules/issues/7017
     - name: Run nf-test
       shell: bash
       env:
-        NFT_DIFF: ${{ env.NFT_DIFF }}
-        NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
         NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
       run: |
         nf-test test \
           --profile=+${{ inputs.profile }} \
-          --tap=test.tap \
-          --verbose \
+          $(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \
           --ci \
           --changed-since HEAD^ \
+          --verbose \
+          --tap=test.tap \
           --shard ${{ inputs.shard }}/${{ inputs.total_shards }}
 
           # Save the absolute path of the test.tap file to the output

.github/workflows/branch.yml

@@ -21,7 +21,7 @@ jobs:
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
       - name: Post PR comment
         if: failure()
-        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
+        uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3
         with:
           message: |
             ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:

.github/workflows/clean-up.yml

@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9
+      - uses: actions/stale@b5d41d4e1d5dceea10e7104786b73624c18a190f # v10
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core 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 contributor. Remove stale label or add a comment if it is still useful."