Skip to content

Commit

Permalink
Merge pull request #911 from nf-core/dev
Browse files Browse the repository at this point in the history
Patch release 2.4.5
  • Loading branch information
TCLamnidis authored Aug 2, 2022
2 parents e582655 + 274d8c0 commit 42c9d5f
Show file tree
Hide file tree
Showing 18 changed files with 329 additions and 355 deletions.
4 changes: 2 additions & 2 deletions .github/workflows/ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down
20 changes: 7 additions & 13 deletions .github/workflows/linting.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand All @@ -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

Expand All @@ -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: |
Expand All @@ -129,4 +124,3 @@ jobs:
lint_log.txt
lint_results.md
PR_number.txt
7 changes: 7 additions & 0 deletions .github/yamllint.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
rules:
document-start: disable
comments: disable
truthy: disable
line-length: disable
empty-lines: disable

14 changes: 14 additions & 0 deletions .gitpod.yml
Original file line number Diff line number Diff line change
@@ -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
2 changes: 1 addition & 1 deletion .nf-core-lint.yml
Original file line number Diff line number Diff line change
Expand Up @@ -3,4 +3,4 @@ files_unchanged:
- .github/CONTRIBUTING.md
- .github/ISSUE_TEMPLATE/bug_report.md
- docs/README.md

- .github/workflows/linting.yml
26 changes: 26 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -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`
Expand Down
4 changes: 2 additions & 2 deletions Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -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
Loading

0 comments on commit 42c9d5f

Please sign in to comment.