Merge branch 'dev' of https://github.com/nf-cmgg/germline into dev

.github/CONTRIBUTING.md

@@ -52,9 +52,9 @@ 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`.
 - Fix the bug, and bump version (X.Y.Z+1).
-- A PR should be made on `master` from patch to directly this particular bug.
+- A PR should be made on `main` from patch to directly this particular bug.
 
 ## Pipeline contribution conventions
 

.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-cmgg/germline/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-cmgg/germline/tree/main/.github/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-cmgg/germline/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-cmgg/germline/tree/main/.github/CONTRIBUTING.md)
 - [ ] 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>`).

.github/workflows/branch.yml

@@ -1,15 +1,15 @@
 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 branch on the repository
+# It fails when someone tries to make a PR against the nf-core `main` branch instead of `dev`
 on:
   pull_request_target:
-    branches: [master]
+    branches: [main]
 
 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 branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
         if: github.repository == 'nf-cmgg/germline'
         run: |
@@ -22,7 +22,7 @@ jobs:
         uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         with:
           message: |
-            ## This PR is against the `master` branch :x:
+            ## This PR is against the `main` branch :x:
 
             * Do not close this PR
             * Click _Edit_ and change the `base` to `dev`
@@ -32,9 +32,9 @@ 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 }}) `main` branch.
+            The `main` branch on nf-core repositories should always contain code from the latest release.
+            Because of this, PRs to `main` 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/build-docs.yml

@@ -2,7 +2,6 @@ name: build docs
 on:
   push:
     branches:
-      - master
       - main
       - dev
 permissions:

.github/workflows/ci.yml

@@ -24,7 +24,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "23.10.0"
+          - "24.04.0"
           - "latest-everything"
         test:
           - "pipeline_default"

.github/workflows/download_pipeline.yml

@@ -2,7 +2,7 @@ name: Test successful pipeline download with 'nf-core 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 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:
@@ -17,10 +17,10 @@ on:
       - edited
       - synchronize
     branches:
-      - master
+      - main
   pull_request_target:
     branches:
-      - master
+      - main
 
 env:
   NXF_ANSI_LOG: false

.github/workflows/linting.yml

@@ -1,6 +1,6 @@
 name: nf-core linting
 # This workflow is triggered on pushes and PRs to the repository.
-# It runs the `nf-core lint` and markdown lint tests to ensure
+# It runs the `nf-core pipelines lint` and markdown lint tests to ensure
 # that the code meets the nf-core guidelines.
 on:
   push:
@@ -41,17 +41,24 @@ jobs:
           python-version: "3.12"
           architecture: "x64"
 
+      - name: read .nf-core.yml
+        uses: pietrobolcato/[email protected]
+        id: read_yml
+        with:
+          config: ${{ github.workspace }}/.nf-core.yaml
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install nf-core
+          pip install git+https://github.com/nf-core/tools@dev
+          #pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
 
-      - name: Run nf-core lint
+      - name: Run nf-core pipelines lint
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
-        run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
+        run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Save PR number
         if: ${{ always() }}

.github/workflows/linting_comment.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
+        uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6
         with:
           workflow: linting.yml
           workflow_conclusion: completed

.nf-core.yml

@@ -1,24 +1,35 @@
 lint:
   files_exist:
-    - CODE_OF_CONDUCT.md
-    - assets/nf-core-germline_logo_light.png
-    - docs/images/nf-core-germline_logo_light.png
-    - docs/images/nf-core-germline_logo_dark.png
-    - .github/ISSUE_TEMPLATE/config.yml
-    - .github/workflows/awstest.yml
-    - .github/workflows/awsfulltest.yml
+    - "CODE_OF_CONDUCT.md"
+    - "assets/nf-core-germline_logo_light.png"
+    - "docs/images/nf-core-germline_logo_light.png"
+    - "docs/images/nf-core-germline_logo_dark.png"
+    - ".github/ISSUE_TEMPLATE/config.yml"
+    - ".github/workflows/awstest.yml"
+    - ".github/workflows/awsfulltest.yml"
+    - "docs/README.md"
   files_unchanged:
-    - CODE_OF_CONDUCT.md
-    - assets/nf-core-germline_logo_light.png
-    - docs/images/nf-core-germline_logo_light.png
-    - docs/images/nf-core-germline_logo_dark.png
-    - .github/ISSUE_TEMPLATE/bug_report.yml
-  multiqc_config:
-    - report_comment
+    - ".github/CONTRIBUTING.md"
+    - ".github/PULL_REQUEST_TEMPLATE.md"
+    - ".github/workflows/branch.yml"
+    - ".github/workflows/linting_comment.yml"
+    - ".github/workflows/linting.yml"
+    - "CODE_OF_CONDUCT.md"
+    - ".github/ISSUE_TEMPLATE/bug_report.yml"
+    - ".prettierignore"
   nextflow_config:
-    - manifest.name
-    - manifest.homePage
-nf_core_version: 2.14.1
+    - "custom_config" # TODO Remove this once the new methods are supported
+    - "manifest.name"
+    - "manifest.homePage"
+    - "params.genomes"
+    - "validation.help.beforeText"
+    - "validation.help.afterText"
+    - "validation.summary.beforeText"
+    - "validation.summary.afterText"
+  multiqc_config:
+    - "report_comment"
+  actions_ci: false # TODO readd this once the linting doesn't act up
+nf_core_version: 3.0.0dev
 repository_type: pipeline
 template:
   author: nvnieuwk

CHANGELOG.md

@@ -3,6 +3,25 @@
 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).
 
+## v1.8.0dev
+
+## New features
+
+1. Added `watchpath` functionality to the pipeline. Add the `watch:` prefix to a file basename in the samplesheet and the pipeline will automatically wait for the file to be created in the `--watchdir` directory (the lookup happens recursively)
+
+## Changes
+
+1. Bumped the minimal support nextflow version to `24.04.0`
+2. Bumped all modules to the newest versions
+3. The pipeline now also outputs `csi` indices
+4. Rename the `master` branch to `main`
+5. Low coverage regions (regions with less than 5 reads) are no longer considered for variant calling
+
+## Refactors
+
+1. Updated the pipeline to the new linting guidelines
+2. Removed `check_max` in favor of `resourceLimits`
+
 ## v1.7.0 - Tolerant Tongeren - [August 9 2024]
 
 ## Fixes

CITATIONS.md

@@ -0,0 +1 @@
+docs/CITATIONS.md

README.md

@@ -2,7 +2,7 @@
 [![GitHub Actions Linting Status](https://github.com/nf-cmgg/germline/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-cmgg/germline/actions/workflows/linting.yml)
 [![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/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.0-23aa62.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/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)

assets/schema_input.json

@@ -16,28 +16,64 @@
                 "meta": ["family"]
             },
             "cram": {
-                "type": "string",
-                "pattern": "^\\S+\\.cram$",
-                "format": "file-path",
-                "exists": true
+                "oneOf": [
+                    {
+                        "type": "string",
+                        "pattern": "^\\S+\\.cram$",
+                        "format": "file-path",
+                        "exists": true
+                    },
+                    {
+                        "type": "string",
+                        "pattern": "^watch:\\S+\\.cram$",
+                        "format": "file-path"
+                    }
+                ]
             },
             "crai": {
-                "type": "string",
-                "pattern": "^\\S+\\.crai$",
-                "format": "file-path",
-                "exists": true
+                "oneOf": [
+                    {
+                        "type": "string",
+                        "pattern": "^\\S+\\.cram\\.crai$",
+                        "format": "file-path",
+                        "exists": true
+                    },
+                    {
+                        "type": "string",
+                        "pattern": "^watch:\\S+\\.cram\\.crai$",
+                        "format": "file-path"
+                    }
+                ]
             },
             "gvcf": {
-                "type": "string",
-                "pattern": "^\\S+vcf(.gz)?$",
-                "format": "file-path",
-                "exists": true
+                "oneOf": [
+                    {
+                        "type": "string",
+                        "pattern": "^\\S+\\.g\\.vcf(\\.gz)?$",
+                        "format": "file-path",
+                        "exists": true
+                    },
+                    {
+                        "type": "string",
+                        "pattern": "^watch:\\S+\\.g\\.vcf(\\.gz)?$",
+                        "format": "file-path"
+                    }
+                ]
             },
             "tbi": {
-                "type": "string",
-                "pattern": "^\\S+\\.tbi$",
-                "format": "file-path",
-                "exists": true
+                "oneOf": [
+                    {
+                        "type": "string",
+                        "pattern": "^\\S+\\.g\\.vcf\\.gz\\.tbi$",
+                        "format": "file-path",
+                        "exists": true
+                    },
+                    {
+                        "type": "string",
+                        "pattern": "^watch:\\S+\\.g\\.vcf\\.gz\\.tbi?$",
+                        "format": "file-path"
+                    }
+                ]
             },
             "roi": {
                 "type": "string",

conf/base.config

@@ -10,40 +10,40 @@
 
 process {
 
-    cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
-    memory = { check_max( 8.GB * task.attempt, 'memory' ) }
-    time   = { check_max( 4.h  * task.attempt, 'time'   ) }
+    cpus   = { 1    * task.attempt }
+    memory = { 8.GB * task.attempt }
+    time   = { 4.h  * task.attempt }
 
     errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
     maxRetries    = 1
     maxErrors     = '-1'
 
     // Process-specific resource requirements
     withLabel:process_single {
-        cpus   = { check_max( 1                  , 'cpus'    ) }
-        memory = { check_max( 8.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
+        cpus   = { 1                     }
+        memory = { 8.GB * task.attempt   }
+        time   = { 4.h  * task.attempt   }
     }
     withLabel:process_low {
-        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 16.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+        cpus   = { 2     * task.attempt  }
+        memory = { 16.GB * task.attempt  }
+        time   = { 4.h   * task.attempt  }
     }
     withLabel:process_medium {
-        cpus   = { check_max( 4     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 32.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
+        cpus   = { 4     * task.attempt  }
+        memory = { 32.GB * task.attempt  }
+        time   = { 8.h   * task.attempt  }
     }
     withLabel:process_high {
-        cpus   = { check_max( 8     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 64.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 16.h  * task.attempt, 'time'    ) }
+        cpus   = { 8     * task.attempt  }
+        memory = { 64.GB * task.attempt  }
+        time   = { 16.h  * task.attempt  }
     }
     withLabel:process_long {
-        time   = { check_max( 20.h  * task.attempt, 'time'    ) }
+        time   = { 20.h  * task.attempt  }
     }
     withLabel:process_high_memory {
-        memory = { check_max( 200.GB * task.attempt, 'memory' ) }
+        memory = { 200.GB * task.attempt }
     }
     withLabel:error_ignore {
         errorStrategy = 'ignore'

conf/empty.config

@@ -0,0 +1 @@
+// DON'T REMOVE THIS FILE

conf/empty_genomes.config

@@ -0,0 +1,3 @@
+// DON'T REMOVE THIS FILE!
+
+params.genomes = [:]