Merge branch 'dev' into fix_datapath_in_nftests

.devcontainer/devcontainer.json

@@ -10,15 +10,7 @@
         "vscode": {
             // Set *default* container specific settings.json values on container create.
             "settings": {
-                "python.defaultInterpreterPath": "/opt/conda/bin/python",
-                "python.linting.enabled": true,
-                "python.linting.pylintEnabled": true,
-                "python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
-                "python.formatting.yapfPath": "/opt/conda/bin/yapf",
-                "python.linting.flake8Path": "/opt/conda/bin/flake8",
-                "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
-                "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
-                "python.linting.pylintPath": "/opt/conda/bin/pylint"
+                "python.defaultInterpreterPath": "/opt/conda/bin/python"
             },
 
             // Add the IDs of extensions you want installed when the container is created.

.github/CONTRIBUTING.md

@@ -9,9 +9,8 @@ Please use the pre-filled template to save time.
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
-:::info
-If you need help using or modifying nf-core/sarek then the best place to ask is on the nf-core Slack [#sarek](https://nfcore.slack.com/channels/sarek) channel ([join our Slack here](https://nf-co.re/join/slack)).
-:::
+> [!NOTE]
+> If you need help using or modifying nf-core/sarek then the best place to ask is on the nf-core Slack [#sarek](https://nfcore.slack.com/channels/sarek) channel ([join our Slack here](https://nf-co.re/join/slack)).
 
 ## Contribution workflow
 
@@ -27,8 +26,11 @@ 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>`.
+You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command:
+
+```bash
+nf-test test --profile debug,test,docker --verbose
+```
 
 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.
@@ -90,7 +92,7 @@ Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
 
 Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
 
-The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block.
+The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.
 
 ### Naming schemes
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/sare
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)
 - [ ] 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>`).
+- [ ] Ensure the test suite passes (`nf-test test tests/ --verbose --profile +docker`).
 - [ ] 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.

.github/workflows/ci.yml

@@ -68,7 +68,7 @@ jobs:
 
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@v4
 
       - name: Hash Github Workspace
         id: hash_workspace
@@ -87,7 +87,7 @@ jobs:
         run: pip install --upgrade -r tests/requirements.txt
 
       - name: Install Nextflow ${{ matrix.NXF_VER }}
-        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+        uses: nf-core/setup-nextflow@v1
         with:
           version: "${{ matrix.NXF_VER }}"
 
@@ -146,7 +146,7 @@ jobs:
         run: conda clean -a
 
       - name: Disk space cleanup
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+        uses: jlumbroso/free-disk-space@v1.3.1
 
       - name: Run pytest-workflow
         uses: Wandalen/wretry.action@v1
@@ -246,7 +246,7 @@ jobs:
           java-version: "17"
 
       - name: Install Nextflow ${{ matrix.NXF_VER }}
-        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+        uses: nf-core/setup-nextflow@v1
         with:
           version: "${{ matrix.NXF_VER }}"
 
@@ -304,7 +304,7 @@ jobs:
           nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64
 
       - name: Disk space cleanup
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+        uses: jlumbroso/free-disk-space@v1.3.1
 
       # Test the module
       - name: Run nf-test

.github/workflows/download_pipeline.yml

@@ -28,7 +28,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+        uses: nf-core/setup-nextflow@v1
 
       - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:

.github/workflows/linting.yml

@@ -35,7 +35,7 @@ jobs:
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+        uses: nf-core/setup-nextflow@v1
 
       - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:

.github/workflows/release-announcements.yml

@@ -12,7 +12,7 @@ jobs:
       - name: get topics and convert to hashtags
         id: get_topics
         run: |
-          curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' > $GITHUB_OUTPUT
+          curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' >> $GITHUB_OUTPUT
 
       - uses: rzr/fediverse-action@master
         with:

.gitpod.yml

@@ -10,13 +10,11 @@ tasks:
 
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
-    - codezombiech.gitignore # Language support for .gitignore files
-    # - cssho.vscode-svgviewer                 # SVG viewer
     - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
-    - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed
     - 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
+    # - 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

.nf-core.yml

@@ -10,6 +10,7 @@ lint:
     - lib/WorkflowSarek.groovy
   files_unchanged:
     - .gitignore
+    - .github/PULL_REQUEST_TEMPLATE.md
     - assets/nf-core-sarek_logo_light.png
     - docs/images/nf-core-sarek_logo_dark.png
     - docs/images/nf-core-sarek_logo_light.png

.prettierignore

@@ -10,3 +10,5 @@ testing/
 testing*
 *.pyc
 bin/
+modules/nf-core/
+subworkflows/nf-core/

CHANGELOG.md

@@ -27,6 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1411](https://github.com/nf-core/sarek/pull/1411) - Temporarily disable sentieon related tests
 - [#1419](https://github.com/nf-core/sarek/pull/1419) - Updating GATK to v4.5, and updating samtools to v1.19.2 in GATK/markduplicates.
 - [#1426](https://github.com/nf-core/sarek/pull/1426) - Updating certain modules in order to fix the testdata-path in the nf-tests of those modules. Setting Docker runOptions for params.use_gatk_spark.
+- [#1428](https://github.com/nf-core/sarek/pull/1428) - Sync `TEMPLATE` with `tools` `2.13.1`
 
 ### Fixed
 
@@ -39,6 +40,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1381](https://github.com/nf-core/sarek/pull/1381) - Swap NGSCheckMate bed file for GATK.GRCh37 to one without the `chr` prefix
 - [#1383](https://github.com/nf-core/sarek/pull/1383) - Fix `--three_prime_clip_r{1,2}` parameter documentation
 - [#1390](https://github.com/nf-core/sarek/pull/1390) - Fix badges in README
+- [#1400](https://github.com/nf-core/sarek/pull/1400) - Fixed input channel for ASSESS_SIGNIFICANCE module, updated makegraph to makegraph2.
 - [#1403](https://github.com/nf-core/sarek/pull/1403) - Fix intervals usage with dot in chromosome names
 
 ### Removed

README.md

@@ -10,6 +10,7 @@
 [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/sarek/results)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3476425-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3476425)
+[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
@@ -157,6 +158,7 @@ We thank the following people for their extensive assistance in the development
 - [Malin Larsson](https://github.com/malinlarsson)
 - [Marcel Martin](https://github.com/marcelm)
 - [Nick Smith](https://github.com/nickhsmith)
+- [Nicolas Schcolnicov](https://github.com/nschcolnicov)
 - [Nilesh Tawari](https://github.com/nilesh-tawari)
 - [Olga Botvinnik](https://github.com/olgabot)
 - [Oskar Wacker](https://github.com/WackerO)

conf/modules/controlfreec.config

@@ -50,8 +50,7 @@ process {
         ]
     }
 
-    withName: 'MAKEGRAPH' {
-        ext.args   = { "${params.cf_ploidy}" }
+    withName: 'MAKEGRAPH2' {
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },

conf/modules/post_variant_calling.config

@@ -17,6 +17,7 @@
 process {
 
     withName: 'GERMLINE_VCFS_CONCAT'{
+        ext.args   = { "-a" }
         ext.when   = { params.concatenate_vcfs }
         publishDir = [
             //specify to avoid publishing, overwritten otherwise

modules.json

@@ -107,11 +107,10 @@
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
-                    "controlfreec/makegraph": {
+                    "controlfreec/makegraph2": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/controlfreec/makegraph/controlfreec-makegraph.diff"
+                        "git_sha": "a7bae48d8bccfae99e3b862fa07bbd50a8df6b82",
+                        "installed_by": ["modules"]
                     },
                     "deepvariant": {
                         "branch": "master",
@@ -327,7 +326,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "ccacf6f5de6df3bc6d73b665c1fd2933d8bbc290",
+                        "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
                         "installed_by": ["modules"]
                     },
                     "ngscheckmate/ncm": {
@@ -491,17 +490,17 @@
                     },
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "cd08c91373cd00a73255081340e4914485846ba1",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "262b17ed2aad591039f914951659177e6c39a8d8",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {
                         "branch": "master",
-                        "git_sha": "cd08c91373cd00a73255081340e4914485846ba1",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["subworkflows"]
                     },
                     "vcf_annotate_ensemblvep": {