Merge pull request #911 from nf-core/dev

Patch release 2.4.5

Author: TCLamnidis

.github/workflows/ci.yml

@@ -37,13 +37,13 @@ jobs:
 
       - name: Build new docker image
         if: env.MATCHED_FILES
-        run: docker build --no-cache . -t nfcore/eager:2.4.4
+        run: docker build --no-cache . -t nfcore/eager:2.4.5
 
       - name: Pull docker image
         if: ${{ !env.MATCHED_FILES }}
         run: |
           docker pull nfcore/eager:dev
-          docker tag nfcore/eager:dev nfcore/eager:2.4.4
+          docker tag nfcore/eager:dev nfcore/eager:2.4.5
 
       - name: Install Nextflow
         env:

.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
+  

.gitpod.yml

@@ -0,0 +1,14 @@
+image: nfcore/gitpod:latest
+
+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
+    - oderwat.indent-rainbow # Highlight indentation level
+    - streetsidesoftware.code-spell-checker # Spelling checker for source code

.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

@@ -3,6 +3,32 @@
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
+## [2.4.5] - 2022-07-39
+
+### `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)
+- [#879](https://github.com/nf-core/eager/issues/879) Add missing threads parameter for pre-clipping FastQC for single end data that caused insufficient memory in some cases (♥ to @marcel-keller for reporting)
+- [#880](https://github.com/nf-core/eager/issues/880) Fix failure of endorSpy to be cached or reexecuted on resume (♥ to @KathrinNaegele, @TCLamnidis, & @mahesh-panchal for reporting and debugging)
+- [#885](https://github.com/nf-core/eager/issues/885) Specify task memory for all tools in get_software_versions to account for incompatibilty of java with some SGE clusters causing hanging of the process (♥ to @maxibor for reporting)
+- [#887](https://github.com/nf-core/eager/issues/887) Clarify what is considered 'ultra-short' reads in the help text of clip_readlength, for when you may wish to turn of length filtering during AdapterRemoval (♥ to @TCLamnidis for reporting)
+- [#889](https://github.com/nf-core/eager/issues/889) Remove/update parameters from benchmarking test profiles (♥ to @TCLamnidis for reporting)
+- [#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.
+- Made slight correction on metro map diagram regarding input data to SexDeterrmine (only BAM trimming output files)
+
+### `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
 
 ### `Added`

Dockerfile

@@ -7,7 +7,7 @@ COPY environment.yml /
 RUN conda env create --quiet -f /environment.yml && conda clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-eager-2.4.4/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.4.5/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-eager-2.4.4 > nf-core-eager-2.4.4.yml
+RUN conda env export --name nf-core-eager-2.4.5 > nf-core-eager-2.4.5.yml