refactor preprocessing, one more time

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -1,4 +1,3 @@
-
 name: Bug report
 description: Report something that is broken or incorrect
 labels: bug

.github/workflows/awsfulltest.yml

@@ -18,7 +18,7 @@ jobs:
         # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
-        
+
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

.github/workflows/awstest.yml

@@ -12,7 +12,6 @@ jobs:
     steps:
       - name: Launch workflow via tower
         uses: nf-core/tower-action@v2
-
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

.github/workflows/ci.yml

@@ -66,7 +66,7 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       - name: Run pipeline with tests settings
-        run: pytest --tag ${{ matrix.test }} --kwdof
+        run: pytest --tag ${{ matrix.test }} --kwdof --git-aware
 
       - name: Output log on failure
         if: failure()

.github/workflows/linting.yml

@@ -12,9 +12,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - uses: actions/setup-node@v1
+      - uses: actions/setup-node@v2
         with:
-          node-version: '10'
+          node-version: '17'
       - name: Install markdownlint
         run: npm install -g markdownlint-cli
       - name: Run Markdownlint
@@ -51,9 +51,9 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: actions/setup-node@v1
+      - uses: actions/setup-node@v2
         with:
-          node-version: '10'
+          node-version: '17'
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -65,13 +65,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v1
-      - uses: actions/setup-node@v1
+      - uses: actions/setup-node@v2
         with:
-          node-version: '10'
+          node-version: '17'
       - name: Install yaml-lint
         run: npm install -g yaml-lint
       - name: Run yaml-lint
-        run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml" -o -name "*.yaml")
+        run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml" -o -name "*.yaml") -c ${GITHUB_WORKSPACE}/.yamllint.yml
 
       # If the above check failed, post a comment on the PR explaining the failure
       - name: Post PR comment
@@ -87,7 +87,7 @@ jobs:
             * Install `yaml-lint`
                 * [Install `npm`](https://www.npmjs.com/get-npm) then [install `yaml-lint`](https://www.npmjs.com/package/yaml-lint) (`npm install -g yaml-lint`)
             * Fix the markdown errors
-                * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml")`
+                * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml") -c ./.yamllint.yml`
                 * Fix any reported errors in your YAML files
 
             Once you push these changes the test should pass, and you can hide this comment :+1:
@@ -120,7 +120,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install nf-core
+          pip install git+https://github.com/nf-core/tools.git@dev
 
       - name: Run nf-core lint
         env:
@@ -142,4 +142,3 @@ jobs:
             lint_log.txt
             lint_results.md
             PR_number.txt
-

.github/workflows/linting_comment.yml

@@ -2,7 +2,6 @@
 name: nf-core linting comment
 # This workflow is triggered after the linting action is complete
 # It posts an automated comment to the PR, even if the PR is coming from a fork
-
 on:
   workflow_run:
     workflows: ["nf-core linting"]

.github/workflows/local_modules.yml

@@ -1,6 +1,5 @@
 name: Local Modules pytest-workflow
 on: [push, pull_request]
-
 jobs:
   changes:
     name: Check for changes

.nf-core.yml

@@ -1,6 +1,9 @@
+repository_type: pipeline
 lint:
   files_unchanged:
+    - .github/workflows/branch.yml
     - .github/workflows/linting.yml
+    - .github/workflows/linting_comment.yml
     - assets/multiqc_config.yaml
     - assets/nf-core-sarek_logo_light.png
     - docs/images/nf-core-sarek_logo_dark.png

.yamllint.yml

@@ -0,0 +1,6 @@
+extends: default
+
+rules:
+    document-start: disable
+    line-length: disable
+    truthy: disable

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) Maxime Garcia, Szilveszter Juhos
+Copyright (c) Maxime Garcia, Szilveszter Juhos, Friederike Hanssen
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -132,7 +132,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 ## Citations
 
 If you use `nf-core/sarek` for your analysis, please cite the `Sarek` article as follows:
-> Garcia M, Juhos S, Larsson M et al. **Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants [version 2; peer review: 2 approved]** *F1000Research* 2020, 9:63 [doi: 10.12688/f1000research.16665.2](http://dx.doi.org/10.12688/f1000research.16665.2).
+> Garcia M, Juhos S, Larsson M et al. **Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants [version 2; peer review: 2 approved]** _F1000Research_ 2020, 9:63 [doi: 10.12688/f1000research.16665.2](http://dx.doi.org/10.12688/f1000research.16665.2).
 
 You can cite the sarek zenodo record for a specific version using the following [doi: 10.5281/zenodo.3476426](https://zenodo.org/badge/latestdoi/184289291)