reintroduce nf-core lint support + update all modules

.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/action-read-yaml@1.0.0
+        id: read_yml
+        with:
+          config: ${{ github.workspace }}/.nf-core.yaml
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install git+https://github.com/nf-core/tools@dev
+          #pip install nf-core==${{ 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 +1,34 @@
 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/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

@@ -8,6 +8,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## 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
 
 ## Refactors
 

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/)

conf/empty.config

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

conf/empty_genomes.config

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

conf/modules.config

@@ -333,7 +333,7 @@ process {
             }
 
             withName: "^.*CRAM_CALL_VARDICTJAVA:VCF_FILTER_BCFTOOLS:FILTER_2\$" {
-                ext.args = "--soft-filter 'LowFreqBias' --mode '+' -e  'FORMAT/AF[0] < 0.02 && FORMAT/VD[0] < 30 && INFO/SBF < 0.1 && INFO/NM >= 2.0' --output-type z"
+                ext.args = "--soft-filter 'LowFreqBias' --mode '+' -e  'FORMAT/AF[0:*] < 0.02 && FORMAT/VD[0] < 30 && INFO/SBF < 0.1 && INFO/NM >= 2.0' --output-type z"
                 ext.prefix = enableOutput("filter") ? final_prefix : {"${meta.id}.filtered"}
                 publishDir  = [
                     overwrite: true,

conf/nf_test.config

@@ -28,4 +28,4 @@ process {
         memory: 6.GB,
         time  : 6.h
     ]
-}
+}

conf/test_full.config

@@ -15,9 +15,7 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
-    // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
-    // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
+    // input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
 
     // Genome references
     genome = 'R64-1-1'

main.nf

@@ -194,7 +194,7 @@ workflow {
 
     def multiqc_logo = params.multiqc_logo   ?: "$projectDir/assets/CMGG_logo.png"
 
-
+    print(params.genomes)
     //
     // SUBWORKFLOW: Run initialisation tasks
     //