perf: bump datavzrd wrapper to 2.6.0 and general bug fixes #548
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#name: My build action requiring more space | |
#on: push | |
# | |
#jobs: | |
# build: | |
# name: Build my artifact | |
# runs-on: ubuntu-latest | |
# steps: | |
# - name: Maximize build space | |
# uses: easimon/maximize-build-space@master | |
# with: | |
# root-reserve-mb: 512 | |
# swap-size-mb: 1024 | |
# remove-dotnet: 'true' | |
# remove-android: 'true' | |
# remove-haskell: 'true' | |
# - name: Checkout | |
# uses: actions/checkout@v2 | |
# | |
# - name: Build | |
# run: | | |
# echo "Free space:" | |
# df -h | |
# echo "free space in ${{ github.workspace }}" | |
# du -hs $(ls -A) ${{ github.workspace }}/* | |
# rm -rf ${{ github.workspace }}/* | |
# echo "free space in .test" | |
# du -hs $(ls -A) .test/* | |
name: Tests | |
on: | |
push: | |
branches: | |
- main | |
pull_request: | |
branches_ignore: [] | |
jobs: | |
formatting: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v1 | |
- name: Formatting | |
uses: github/super-linter@v4 | |
env: | |
VALIDATE_ALL_CODEBASE: false | |
DEFAULT_BRANCH: main | |
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
VALIDATE_SNAKEMAKE_SNAKEFMT: true | |
linting: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v1 | |
- name: Linting | |
uses: snakemake/[email protected] | |
with: | |
directory: .test | |
snakefile: workflow/Snakefile | |
args: "--lint" | |
run-rna-workflow: | |
runs-on: ubuntu-latest | |
needs: | |
- linting | |
- formatting | |
steps: | |
- name: Checkout repository | |
uses: actions/checkout@v2 | |
with: | |
submodules: recursive | |
- name: Test workflow | |
uses: snakemake/[email protected] | |
with: | |
directory: .test | |
snakefile: workflow/Snakefile | |
args: "--use-conda --show-failed-logs --cores 1 --conda-cleanup-pkgs cache --all-temp" | |
run-3prime-rna-workflow: | |
runs-on: ubuntu-latest | |
needs: | |
- linting | |
- formatting | |
steps: | |
- name: Checkout repository | |
uses: actions/checkout@v2 | |
with: | |
submodules: recursive | |
- name: Test 3-prime-workflow | |
uses: snakemake/[email protected] | |
with: | |
directory: .test/3-prime-config | |
snakefile: workflow/Snakefile | |
args: "--use-conda --show-failed-logs --cores 1 --conda-cleanup-pkgs cache --all-temp" | |
# Disable report testing for now since we mark all output files as temporary above. | |
# TODO: add some kind of test mode to report generation which does not really try to include | |
# results. | |
# - name: Test report | |
# uses: snakemake/[email protected] | |
# with: | |
# directory: .test | |
# snakefile: workflow/Snakefile | |
# args: "--report report.zip" |