Merge pull request #1360 from nf-core/nf-core-template-merge-2.11

Important! Template update for nf-core/tools v2.11
nf-core · Dec 20, 2023 · 490c68c · 490c68c
2 parents 72a7af6 + ab9ade1
commit 490c68c
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diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -27,6 +27,9 @@ If you're not used to this workflow with git, you can start with some [docs from
 
 ## Tests
 
+You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to
+receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir <OUTDIR>`.
+
 When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
 Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
 

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -19,6 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/sare
 - [ ] If necessary, also make a PR on the nf-core/sarek _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core 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>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `CHANGELOG.md` is updated.

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -28,7 +28,7 @@ jobs:
       # Expose matched filters as job 'tags' output variable
       tags: ${{ steps.filter.outputs.changes }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: frouioui/paths-filter@main
         id: filter
@@ -59,7 +59,7 @@ jobs:
 
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Hash Github Workspace
         id: hash_workspace
@@ -105,7 +105,7 @@ jobs:
 
       - name: Check out test data
         if: steps.cache-testdata.outputs.cache-hit != 'true'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: nf-core/test-datasets
           ref: sarek3
@@ -168,7 +168,7 @@ jobs:
       tags: ${{ steps.filter.outputs.changes }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Combine all tags.yml files
         id: get_tags
@@ -208,6 +208,7 @@ jobs:
           - tags: "dragmap/align"
           - tags: "fastp"
           - tags: "fastqc"
+          - tags: "multiqc"
           - tags: "samtools/stats"
           - tags: "untar"
     env:
@@ -216,7 +217,7 @@ jobs:
       SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: actions/setup-java@v3
         with:

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@v3
+      - uses: actions/checkout@v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -24,7 +24,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -14,9 +14,9 @@ jobs:
   EditorConfig:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -27,9 +27,9 @@ jobs:
   Prettier:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install Prettier
         run: npm install -g prettier
@@ -40,7 +40,7 @@ jobs:
   PythonBlack:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Check code lints with Black
         uses: psf/black@stable
@@ -71,7 +71,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1

diff --git a/.gitpod.yml b/.gitpod.yml
@@ -4,7 +4,9 @@ tasks:
     command: |
       pre-commit install --install-hooks
       nextflow self-update
-
+  - name: unset JAVA_TOOL_OPTIONS
+    command: |
+      unset JAVA_TOOL_OPTIONS
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
     - codezombiech.gitignore # Language support for .gitignore files

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#1339](https://github.com/nf-core/sarek/pull/1339) - Update sentieon-modules
 - [#1344](https://github.com/nf-core/sarek/pull/1344) - Enable CRAM QC, when starting from variantcalling
+- [#1360](https://github.com/nf-core/sarek/pull/1360) - Sync `TEMPLATE` with `tools` `2.11`
 
 ### Fixed
 
@@ -31,6 +32,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 | Dependency | Old version | New version |
 | ---------- | ----------- | ----------- |
+| multiqc    | 1.17        | 1.18        |
 
 ### Modules / Subworkflows
 

diff --git a/README.md b/README.md
@@ -59,11 +59,8 @@ Depending on the options and samples provided, the pipeline can currently perfor
 
 ## Usage
 
-:::note
-If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how
-to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)
-with `-profile test` before running the workflow on actual data.
-:::
+> [!NOTE]
+> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
 
 First, prepare a samplesheet with your input data that looks as follows:
 
@@ -85,11 +82,9 @@ nextflow run nf-core/sarek \
    --outdir <OUTDIR>
 ```
 
-:::warning
-Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
-provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
-see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
-:::
+> [!WARNING]
+> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
+> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
 
 For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/sarek/usage) and the [parameter documentation](https://nf-co.re/sarek/parameters).
 

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -3,7 +3,7 @@ custom_logo_url: https://github.com/nf-core/sarek/
 custom_logo_title: "nf-core/sarek"
 
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/sarek/releases/tag/dev" target="_blank">nf-core/sarek</a>
+  This report has been generated by the <a href="https://github.com/nf-core/sarek/tree/dev" target="_blank">nf-core/sarek</a>
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://nf-co.re/sarek/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:

diff --git a/docs/usage.md b/docs/usage.md
@@ -58,7 +58,7 @@ with `params.yaml` containing:
 ```yaml
 input: './samplesheet.csv'
 outdir: './results/'
-genome: 'GRCh37'
+genome: 'GATK.GRCh38'
 <...>
 ```
 

diff --git a/modules.json b/modules.json
@@ -152,7 +152,7 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53",
                         "installed_by": ["modules"]
                     },
                     "fgbio/callmolecularconsensusreads": {
@@ -332,7 +332,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "214d575774c172062924ad3564b4f66655600730",
+                        "git_sha": "4ab13872435962dadc239979554d13709e20bf29",
                         "installed_by": ["modules"]
                     },
                     "ngscheckmate/ncm": {

diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf