Merge remote-tracking branch 'upstream/dev' into language-server-fixes

nf-core · Dec 16, 2024 · fe308df · fe308df
2 parents 475dc2a + b0ed0c0
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diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -1,4 +1,4 @@
-# nf-core/mag: Contributing Guidelines
+# `nf-core/mag`: Contributing Guidelines
 
 Hi there!
 Many thanks for taking an interest in improving nf-core/mag.
@@ -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/mag documentation](https://nf-co.re/mag/usage) and don't hesitate to get in touch on the nf-core Slack [#mag](https://nfcore.slack.com/channels/mag) channel ([join our Slack here](https://nf-co.re/join/slack)).
 
 ## Pipeline contribution conventions
 
-To make the nf-core/mag 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/mag` 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`.
 

diff --git a/.github/workflows/awsfulltest.yml b/.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:
@@ -18,19 +19,30 @@ jobs:
     if: github.repository == 'nf-core/mag' && 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 }}'
           CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
           test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
+
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         with:

diff --git a/.github/workflows/branch.yml b/.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/mag'
         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.

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -50,7 +50,7 @@ jobs:
           sudo rm -rf "$AGENT_TOOLSDIRECTORY"
 
       - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
@@ -130,36 +130,3 @@ jobs:
       - name: Run pipeline with ${{ matrix.test_name }} test profile
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},docker --outdir ./results
-
-  checkm:
-    name: Run single test to checkm due to database download
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mag') }}
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Free some space
-        run: |
-          sudo rm -rf "/usr/local/share/boost"
-          sudo rm -rf "$AGENT_TOOLSDIRECTORY"
-
-      - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
-
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Clean up Disk space
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
-
-      - name: Download and prepare CheckM database
-        run: |
-          mkdir -p databases/checkm
-          wget https://zenodo.org/records/7401545/files/checkm_data_2015_01_16.tar.gz -P databases/checkm
-          tar xzvf databases/checkm/checkm_data_2015_01_16.tar.gz -C databases/checkm/
-
-      - name: Run pipeline with ${{ matrix.profile }} test profile
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --binqc_tool checkm --checkm_db databases/checkm
diff --git a/.github/workflows/download_pipeline.yml b/.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:
@@ -17,9 +17,11 @@ on:
       - edited
       - synchronize
     branches:
+      - main
       - master
   pull_request_target:
     branches:
+      - main
       - master
 
 env:
@@ -35,7 +37,7 @@ jobs:
       - 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"
@@ -69,7 +71,7 @@ jobs:
           --outdir ./${{ env.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'
 

diff --git a/.github/workflows/fix-linting.yml b/.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"
 

diff --git a/.github/workflows/linting.yml b/.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: |

diff --git a/.github/workflows/linting_comment.yml b/.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

diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
@@ -31,7 +31,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.10"
       - name: Install dependencies

diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           ref: ${{ github.event.pull_request.head.sha }}
 

diff --git a/.gitpod.yml b/.gitpod.yml
@@ -6,12 +6,5 @@ tasks:
       nextflow self-update
 
 vscode:
-  extensions: # based on nf-core.nf-core-extensionpack
-    #- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
-    - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
-    - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
-    - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
-    - nextflow.nextflow # Nextflow syntax highlighting
-    - oderwat.indent-rainbow # Highlight indentation level
-    - streetsidesoftware.code-spell-checker # Spelling checker for source code
-    - charliermarsh.ruff # Code linter Ruff
+  extensions:
+    - nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,22 +1,19 @@
-bump_version: null
 lint:
   files_unchanged:
     - lib/NfcoreTemplate.groovy
   nextflow_config:
     - config_defaults:
         - params.phix_reference
         - params.lambda_reference
-nf_core_version: 3.0.2
-org_path: null
+nf_core_version: 3.1.0
 repository_type: pipeline
 template:
-  author: "Hadrien Gourlé, Daniel Straub, Sabrina Krakau, James A. Fellows Yates, Maxime Borry"
+  author: "Hadrien Gourlé, Daniel Straub, Sabrina Krakau, James A. Fellows Yates,
+    Maxime Borry"
   description: Assembly, binning and annotation of metagenomes
   force: false
   is_nfcore: true
   name: mag
   org: nf-core
   outdir: .
-  skip_features: null
-  version: 3.3.0dev
-update: null
+  version: 3.3.0
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -0,0 +1,3 @@
+{
+    "markdown.styles": ["public/vscode_markdown.css"]
+}
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,26 +3,37 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## dev [unreleased]
+## 3.3.0 [2024-12-16]
 
 ### `Added`
 
 - [#692](https://github.com/nf-core/mag/pull/692) - Added Nanoq as optional longread filtering tool (added by @muabnezor)
 - [#692](https://github.com/nf-core/mag/pull/692) - Added chopper as optional longread filtering tool and/or phage lambda removal tool (added by @muabnezor)
+- [#707](https://github.com/nf-core/mag/pull/707) - Make Bin QC a subworkflow (added by @dialvarezs)
+- [#707](https://github.com/nf-core/mag/pull/707) - Added CheckM2 as an alternative bin completeness and QC tool (added by @dialvarezs)
 - [#708](https://github.com/nf-core/mag/pull/708) - Added `--exclude_unbins_from_postbinning` parameter to exclude unbinned contigs from post-binning processes, speeding up Prokka in some cases (added by @dialvarezs)
+- [#732](https://github.com/nf-core/mag/pull/732) - Added support for Prokka's compliance mode with `--prokka_with_compliance --prokka_compliance_centre <xyz>` (reported by @audy and @Thomieh73, added by @jfy133)
 
 ### `Changed`
 
+- [#731](https://github.com/nf-core/mag/pull/731) - Updated to nf-core 3.1.0 `TEMPLATE` (by @jfy133)
+
 ### `Fixed`
 
+- [#707](https://github.com/nf-core/mag/pull/708) - Fixed channel passed as GUNC input (added by @dialvarezs)
+- [#724](https://github.com/nf-core/mag/pull/724) - Fix quoting in `utils_nfcore_mag_pipeline/main.nf` (added by @dialvarezs)
 - [#716](https://github.com/nf-core/mag/pull/692) - Make short read processing a subworkflow (added by @muabnezor)
 - [#708](https://github.com/nf-core/mag/pull/708) - Fixed channel passed as GUNC input (added by @dialvarezs)
+- [#729](https://github.com/nf-core/mag/pull/729) - Fixed misspecified multi-FASTQ input for single-end data in MEGAHIT (reported by John Richards, fix by @jfy133)
 
 ### `Dependencies`
 
 | Tool    | Previous version | New version |
 | ------- | ---------------- | ----------- |
+| CheckM  | 1.2.1            | 1.2.3       |
+| CheckM2 |                  | 1.0.2       |
 | chopper |                  | 0.9.0       |
+| GUNC    | 1.0.5            | 1.0.6       |
 | nanoq   |                  | 0.10.0      |
 
 ### `Deprecated`

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -40,6 +40,10 @@
 
   > Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015). CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research, 25(7), 1043–1055. doi: 10.1101/gr.186072.114
 
+- [CheckM2](https://doi.org/10.1038/s41592-023-01940-w)
+
+  > Chklovski, A., Parks, D. H., Woodcroft, B. J., & Tyson, G. W. (2023). CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nature Methods, 20(8), 1203-1212. doi: https://doi.org/10.1038/s41592-023-01940-w
+
 - [Chopper](https://doi.org/10.1093/bioinformatics/bty149)
 
   > De Coster W, D'Hert S, Schultz DT, Cruts M, Van Broeckhoven C. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics. 2018 Aug 1;34(15):2666-2669. doi: 10.1093/bioinformatics/bty149