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main.yaml
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name: Tests
on:
push:
branches:
- master
pull_request:
branches: [ master ]
branches_ignore: []
jobs:
Linting:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v1
- name: Lint workflow
uses: snakemake/snakemake-github-action@v1.19.0
with:
directory: .
snakefile: workflow/Snakefile
args: "--lint"
stagein: |
export TMPDIR=/tmp
Testing:
runs-on: ubuntu-latest
needs: Linting
steps:
- name: Checkout repository
uses: actions/checkout@v1
- name: Test dry run for a large single end workflow
uses: snakemake/snakemake-github-action@v1.19.0
with:
directory: .test
snakefile: workflow/Snakefile
args: "--use-conda -n --show-failed-logs -j 10 --conda-cleanup-pkgs cache --conda-frontend mamba"
- name: Test minimized single end workflow (on local reduced SRA files for a single chromosome - homo sapiens)
uses: snakemake/snakemake-github-action@v1.19.0
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config_single_end_reduced/config.yaml --use-conda --cache --show-failed-logs -j 10 --conda-cleanup-pkgs cache --conda-frontend mamba"
stagein: |
export TMPDIR=/tmp
rm -rf .test/resources .test/results
export SNAKEMAKE_OUTPUT_CACHE=/snakemake-cache
mkdir -p -m a+rw $SNAKEMAKE_OUTPUT_CACHE
#
# # Test for single end reads with larger data sets and download of SRA files. It can be included for heavy duty testing on dedicated machines.
#
# - name: Test single end workflow (test data sra-download)
# uses: snakemake/snakemake-github-action@v1.19.0
# with:
# directory: .test
# snakefile: workflow/Snakefile
# args: "--configfile .test/config_single_end/config.yaml --use-conda --cache --show-failed-logs -j 10 --conda-cleanup-pkgs cache --conda-frontend mamba"
# stagein: |
# export TMPDIR=/tmp
# rm -rf .test/resources .test/results
# export SNAKEMAKE_OUTPUT_CACHE=/snakemake-cache
# mkdir -p -m a+rw $SNAKEMAKE_OUTPUT_CACHE
- name: Test minimized paired end workflow (on local reduced SRA files for a single chromosome - saccharomyces cerevisiae)
uses: snakemake/snakemake-github-action@v1.19.0
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config_paired_end_reduced/config.yaml --use-conda --cache --show-failed-logs -j 10 --conda-cleanup-pkgs cache --conda-frontend mamba"
stagein: |
export TMPDIR=/tmp
rm -rf .test/resources .test/results
export SNAKEMAKE_OUTPUT_CACHE=/snakemake-cache
mkdir -p -m a+rw $SNAKEMAKE_OUTPUT_CACHE
#
# # Test for paired end reads with larger datasets from git submodules. It can be included for heavy duty testing on dedicated machines.
#
# - uses: actions/checkout@v1
# - name: Checkout submodules
# uses: textbook/git-checkout-submodule-action@2.0.0
#
# - name: Test paired end workflow (submodule test data)
# uses: snakemake/snakemake-github-action@v1.19.0
# with:
# directory: .test
# snakefile: workflow/Snakefile
# args: "--configfile .test/config_paired_end/config.yaml --use-conda --cache --show-failed-logs -j 10 --conda-cleanup-pkgs cache --conda-frontend mamba"
# stagein: |
# export TMPDIR=/tmp
# rm -rf .test/resources .test/results
# export SNAKEMAKE_OUTPUT_CACHE=/snakemake-cache
# mkdir -p -m a+rw $SNAKEMAKE_OUTPUT_CACHE
- name: Test report
uses: snakemake/snakemake-github-action@v1.19.0
with:
directory: .test
snakefile: workflow/Snakefile
args: "--report report.zip --configfile .test/config_paired_end_reduced/config.yaml"
stagein: |
export TMPDIR=/tmp
rm -rf .test/resources .test/results