Update template to 3.1.2

.editorconfig

@@ -32,11 +32,12 @@ indent_size = unset
 [*.{py,md}]
 indent_style = unset
 
-[/docs/*.xml*]
-indent_style = unset
-insert_final_newline = unset
-
+# ignore xml files in docs used by metro maps
 [/docs/images/metro/*.xml*]
 indent_style = unset
 insert_final_newline = unset
 end_of_line = unset
+
+# ignore ro-crate metadata files
+[**/ro-crate-metadata.json]
+insert_final_newline = unset

.github/CONTRIBUTING.md

@@ -1,4 +1,4 @@
-# nf-core/phaseimpute: Contributing Guidelines
+# `nf-core/phaseimpute`: Contributing Guidelines
 
 Hi there!
 Many thanks for taking an interest in improving nf-core/phaseimpute.
@@ -55,23 +55,23 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 :warning: Only in the unlikely and regretful event of a release happening with a bug.
 
-- On your own fork, make a new branch `patch` based on `upstream/master`.
+- On your own fork, make a new branch `patch` based on `upstream/main` or `upstream/master`.
 - Fix the bug, and bump version (X.Y.Z+1).
-- A PR should be made on `master` from patch to directly this particular bug.
+- Open a pull-request from `patch` to `main`/`master` with the changes.
 
 ## Getting help
 
 For further information/help, please consult the [nf-core/phaseimpute documentation](https://nf-co.re/phaseimpute/usage) and don't hesitate to get in touch on the nf-core Slack [#phaseimpute](https://nfcore.slack.com/channels/phaseimpute) channel ([join our Slack here](https://nf-co.re/join/slack)).
 
 ## Pipeline contribution conventions
 
-To make the nf-core/phaseimpute code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
+To make the `nf-core/phaseimpute` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
 
 ### Adding a new step
 
 If you wish to contribute a new step, please use the following coding standards:
 
-1. Define the corresponding input channel into your new process from the expected previous process channel
+1. Define the corresponding input channel into your new process from the expected previous process channel.
 2. Write the process block (see below).
 3. Define the output channel if needed (see below).
 4. Add any new parameters to `nextflow.config` with a default (see below).
@@ -84,7 +84,7 @@ If you wish to contribute a new step, please use the following coding standards:
 
 ### Default values
 
-Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
+Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`.
 
 Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`.
 

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -9,7 +9,6 @@ body:
 
         - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
         - [nf-core/phaseimpute pipeline documentation](https://nf-co.re/phaseimpute/usage)
-
   - type: textarea
     id: description
     attributes:

.github/workflows/awsfulltest.yml

@@ -1,11 +1,12 @@
 name: nf-core AWS full size tests
-# This workflow is triggered on PRs opened against the master branch.
+# This workflow is triggered on PRs opened against the main/master branch.
 # It can be additionally triggered manually with GitHub actions workflow dispatch button.
 # It runs the -profile 'test_full' on AWS batch
 
 on:
   pull_request:
     branches:
+      - main
       - master
   workflow_dispatch:
   pull_request_review:
@@ -18,14 +19,24 @@ jobs:
     if: github.repository == 'nf-core/phaseimpute' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
-      - uses: octokit/[email protected]
+      - name: Get PR reviews
+        uses: octokit/[email protected]
         if: github.event_name != 'workflow_dispatch'
         id: check_approvals
+        continue-on-error: true
         with:
           route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      - id: test_variables
+
+      - name: Check for approvals
+        if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
+        run: |
+          echo "No review approvals found. At least 2 approvals are required to run this action automatically."
+          exit 1
+
+      - name: Check for enough approvals (>=2)
+        id: test_variables
         if: github.event_name != 'workflow_dispatch'
         run: |
           JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'

.github/workflows/branch.yml

@@ -1,15 +1,17 @@
 name: nf-core branch protection
-# This workflow is triggered on PRs to master branch on the repository
-# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
+# This workflow is triggered on PRs to `main`/`master` branch on the repository
+# It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev`
 on:
   pull_request_target:
-    branches: [master]
+    branches:
+      - main
+      - master
 
 jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
+      # PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
         if: github.repository == 'nf-core/phaseimpute'
         run: |
@@ -22,7 +24,7 @@ jobs:
         uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         with:
           message: |
-            ## This PR is against the `master` branch :x:
+            ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:
 
             * Do not close this PR
             * Click _Edit_ and change the `base` to `dev`
@@ -32,9 +34,9 @@ jobs:
 
             Hi @${{ github.event.pull_request.user.login }},
 
-            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
-            The `master` branch on nf-core repositories should always contain code from the latest release.
-            Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
+            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) ${{github.event.pull_request.base.ref}} branch.
+            The ${{github.event.pull_request.base.ref}} branch on nf-core repositories should always contain code from the latest release.
+            Because of this, PRs to ${{github.event.pull_request.base.ref}} are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
 
             You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
             Note that even after this, the test will continue to show as failing until you push a new commit.

.github/workflows/ci.yml

@@ -29,7 +29,7 @@ concurrency:
 
 jobs:
   test:
-    name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.TEST_PROFILE }} | ${{ matrix.profile }})"
+    name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
     # Only run on push if this is the nf-core dev branch (merged PRs)
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/phaseimpute') }}"
     runs-on: ubuntu-latest
@@ -40,9 +40,10 @@ jobs:
           - "24.04.2"
           - "latest-everything"
         profile:
+          - "conda"
           - "docker"
           - "singularity"
-        TEST_PROFILE:
+        test_name:
           - "test_all"
           - "test_validate"
           - "test_stitch"
@@ -57,12 +58,9 @@ jobs:
             profile: "singularity"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
-
-      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
-          distribution: "temurin"
-          java-version: "17"
+          fetch-depth: 0
 
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2

.github/workflows/download_pipeline.yml

@@ -2,7 +2,7 @@ name: Test successful pipeline download with 'nf-core pipelines download'
 
 # Run the workflow when:
 #  - dispatched manually
-#  - when a PR is opened or reopened to master branch
+#  - when a PR is opened or reopened to main/master branch
 #  - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev.
 on:
   workflow_dispatch:
@@ -17,25 +17,42 @@ on:
       - edited
       - synchronize
     branches:
+      - main
       - master
   pull_request_target:
     branches:
+      - main
       - master
 
 env:
   NXF_ANSI_LOG: false
 
 jobs:
+  configure:
+    runs-on: ubuntu-latest
+    outputs:
+      REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }}
+      REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }}
+      REPO_BRANCH: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }}
+    steps:
+      - name: Get the repository name and current branch
+        id: get_repo_properties
+        run: |
+          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
+          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
+          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"
+
   download:
     runs-on: ubuntu-latest
+    needs: configure
     steps:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           architecture: "x64"
@@ -50,12 +67,6 @@ jobs:
           python -m pip install --upgrade pip
           pip install git+https://github.com/nf-core/tools.git@dev
 
-      - name: Get the repository name and current branch set as environment variable
-        run: |
-          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV}
-          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
-          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
-
       - name: Make a cache directory for the container images
         run: |
           mkdir -p ./singularity_container_images
@@ -64,55 +75,59 @@ jobs:
         env:
           NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
         run: |
-          nf-core pipelines download ${{ env.REPO_LOWERCASE }} \
-          --revision ${{ env.REPO_BRANCH }} \
-          --outdir ./${{ env.REPOTITLE_LOWERCASE }} \
+          nf-core pipelines download ${{ needs.configure.outputs.REPO_LOWERCASE }} \
+          --revision ${{ needs.configure.outputs.REPO_BRANCH }} \
+          --outdir ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} \
           --compress "none" \
           --container-system 'singularity' \
-          --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \
+          --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \
           --container-cache-utilisation 'amend' \
           --download-configuration 'yes'
 
       - name: Inspect download
-        run: tree ./${{ env.REPOTITLE_LOWERCASE }}
+        run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}
+
+      - name: Inspect container images
+        run: tree ./singularity_container_images | tee ./container_initial
 
       - name: Count the downloaded number of container images
         id: count_initial
         run: |
           image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
           echo "Initial container image count: $image_count"
-          echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV}
+          echo "IMAGE_COUNT_INITIAL=$image_count" >> "$GITHUB_OUTPUT"
 
       - name: Run the downloaded pipeline (stub)
         id: stub_run_pipeline
         continue-on-error: true
         env:
           NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
+        run: nextflow run ./${{needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
       - name: Run the downloaded pipeline (stub run not supported)
         id: run_pipeline
-        if: ${{ job.steps.stub_run_pipeline.status == failure() }}
+        if: ${{ steps.stub_run_pipeline.outcome == 'failure' }}
         env:
           NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
+        run: nextflow run ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -profile test,singularity --outdir ./results
 
       - name: Count the downloaded number of container images
         id: count_afterwards
         run: |
           image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
           echo "Post-pipeline run container image count: $image_count"
-          echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV}
+          echo "IMAGE_COUNT_AFTER=$image_count" >> "$GITHUB_OUTPUT"
 
       - name: Compare container image counts
         run: |
-          if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then
-            initial_count=${{ env.IMAGE_COUNT_INITIAL }}
-            final_count=${{ env.IMAGE_COUNT_AFTER }}
+          if [ "${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}" -ne "${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}" ]; then
+            initial_count=${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}
+            final_count=${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}
             difference=$((final_count - initial_count))
             echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!"
-            tree ./singularity_container_images
+            tree ./singularity_container_images > ./container_afterwards
+            diff ./container_initial ./container_afterwards
             exit 1
           else
             echo "The pipeline can be downloaded successfully!"

.github/workflows/fix-linting.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,7 +32,7 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 

.github/workflows/linting.yml

@@ -14,10 +14,10 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
@@ -31,12 +31,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           architecture: "x64"
@@ -74,7 +74,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
+        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
         with:
           name: linting-logs
           path: |

.github/workflows/linting_comment.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6
+        uses: dawidd6/action-download-artifact@80620a5d27ce0ae443b965134db88467fc607b43 # v7
         with:
           workflow: linting.yml
           workflow_conclusion: completed