Merge branch 'dev' into endorspy-resume-fix

Author: jfy133

.github/workflows/linting.yml

@@ -12,9 +12,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - uses: actions/setup-node@v1
-        with:
-          node-version: '10'
+      - uses: actions/setup-node@v2
+
       - name: Install markdownlint
         run: npm install -g markdownlint-cli
       - name: Run Markdownlint
@@ -46,18 +45,16 @@ jobs:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           allow-repeats: false
 
-
   YAML:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v1
-      - uses: actions/setup-node@v1
-        with:
-          node-version: '10'
+      - uses: actions/setup-node@v2
+
       - 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/yamllint.yml
 
       # If the above check failed, post a comment on the PR explaining the failure
       - name: Post PR comment
@@ -84,11 +81,9 @@ jobs:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           allow-repeats: false
 
-
   nf-core:
     runs-on: ubuntu-latest
     steps:
-
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
@@ -101,8 +96,8 @@ jobs:
 
       - uses: actions/setup-python@v1
         with:
-          python-version: '3.6'
-          architecture: 'x64'
+          python-version: "3.6"
+          architecture: "x64"
 
       - name: Install dependencies
         run: |
@@ -129,4 +124,3 @@ jobs:
             lint_log.txt
             lint_results.md
             PR_number.txt
-

.github/yamllint.yml

@@ -0,0 +1,7 @@
+rules:
+  document-start: disable
+  comments: disable
+  truthy: disable
+  line-length: disable
+  empty-lines: disable
+  

.nf-core-lint.yml

@@ -3,4 +3,4 @@ files_unchanged:
   - .github/CONTRIBUTING.md
   - .github/ISSUE_TEMPLATE/bug_report.md
   - docs/README.md
-
+  - .github/workflows/linting.yml

CHANGELOG.md

@@ -7,7 +7,6 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Added`
 
-
 ### `Fixed`
 
 - [#882](https://github.com/nf-core/eager/pull/882) Define DSL1 execution explicitly, as new versions Nextflow made DSL2 default (♥ to & fix from @Lehmann-Fabian)
@@ -19,10 +18,14 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - [#895](https://github.com/nf-core/eager/issues/895) Output documentation typo fix and added location of output docs in pipeline summary (♥ to @RodrigoBarquera for reporting)
 - [#897](https://github.com/nf-core/eager/issues/897) Fix pipeline crash if no Kraken2 results generated (♥ to @alexandregilardet for reporting)
 - [#899](https://github.com/nf-core/eager/issues/897) Fix pipeline crash for circulargenerator if reference file does not end in .fasta (♥ to @scarlhoff for reporting)
+- Fixed some missing default values in the nextflow parameter schema JSON
+- [#789](https://github.com/nf-core/eager/issues/789) Substantial speed and memory optimisation of the `extract_map_reads.py` script (♥ to @ivelsko for reporting, @maxibor for optimisation)
 - Fix staging of input bams for genotyping_pileupcaller process. Downstream changes from changes introduced when fixing endorspy caching.
 
 ### `Dependencies`
 
+- Updated MultiQC to latest stable alpha version on bioconda, correcting the previously nonsensical AdapterRemoval plots (♥ to @NiemannJ for fixing in MultiQC)
+
 ### `Deprecated`
 
 ## [2.4.4] - 2022-04-08