Important! Template update for nf-core/tools v4.0.3

.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-core/rnasplice devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt

.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-core/rnasplice/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/rnasplice/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-core/rnasplice/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-core/rnasplice/tree/master/docs/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/rnasplice _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).

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

@@ -21,7 +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

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

@@ -20,24 +20,24 @@ 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@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
       with:
-        python-version: "3.13"
+        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@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0
 
     - name: Set up Singularity
       if: contains(inputs.profile, 'singularity')
@@ -48,19 +48,17 @@ runs:
 
     - name: Conda setup
       if: contains(inputs.profile, 'conda')
-      uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3
+      uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4
       with:
         auto-update-conda: true
         conda-solver: libmamba
+        channels: conda-forge
+        channel-priority: strict
         conda-remove-defaults: true
 
-      # 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 \

.github/workflows/awsfulltest.yml

@@ -23,26 +23,45 @@ jobs:
           echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT"
 
       - name: Launch workflow via Seqera Platform
-        uses: seqeralabs/action-tower-launch@v2
+        uses: seqeralabs/action-tower-launch@51565b514bff1827cf34620de25d0055759f1fc9 # v2
         # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
         with:
-          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          compute_env: ${{ vars.TOWER_COMPUTE_ENV }}
           revision: ${{ steps.revision.outputs.revision }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnasplice/work-${{ steps.revision.outputs.revision }}
+          workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/rnasplice/work-${{ steps.revision.outputs.revision }}
+          nextflow_config: |
+            plugins {
+              id 'nf-slack@0.5.0'
+            }
+            slack {
+              enabled = true
+              bot {
+                token = '${{ secrets.NFSLACK_BOT_TOKEN }}'
+                channel = 'rnasplice'
+              }
+              onStart {
+                enabled = false
+              }
+              onComplete {
+                message = ':white_check_mark: *rnasplice/test_full* completed successfully! :tada:'
+              }
+              onError {
+                message = ':x: *rnasplice/test_full* failed :crying_cat_face:'
+              }
+            }
           parameters: |
             {
-              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnasplice/results-${{ steps.revision.outputs.revision }}"
+              "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/rnasplice/results-${{ steps.revision.outputs.revision }}"
             }
           profiles: test_full
 
-      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: Seqera Platform debug log file
           path: |
-            seqera_platform_action_*.log
-            seqera_platform_action_*.json
+            tower_action_*.log
+            tower_action_*.json

.github/workflows/awstest.yml

@@ -12,22 +12,22 @@ jobs:
     steps:
       # Launch workflow using Seqera Platform CLI tool action
       - name: Launch workflow via Seqera Platform
-        uses: seqeralabs/action-tower-launch@v2
+        uses: seqeralabs/action-tower-launch@51565b514bff1827cf34620de25d0055759f1fc9 # v2
         with:
-          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          compute_env: ${{ vars.TOWER_COMPUTE_ENV }}
           revision: ${{ github.sha }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnasplice/work-${{ github.sha }}
+          workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/rnasplice/work-${{ github.sha }}
           parameters: |
             {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnasplice/results-test-${{ github.sha }}"
+              "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/rnasplice/results-test-${{ github.sha }}"
             }
           profiles: test
 
-      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: Seqera Platform debug log file
           path: |
-            seqera_platform_action_*.log
-            seqera_platform_action_*.json
+            tower_action_*.log
+            tower_action_*.json