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ashleys-qc-pipeline workflow checks

Minor update #5

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Minor update

Minor update #5

Workflow file for this run

.github/workflows/main_test.yaml at 9531c3a
name: ashleys-qc-pipeline workflow checks
on:
push:
branches:
- "**"
jobs:
# WORK
Formatting:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Formatting
uses: github/super-linter@v4
env:
VALIDATE_ALL_CODEBASE: false
DEFAULT_BRANCH: master
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
VALIDATE_SNAKEMAKE_SNAKEFMT: true
Linting:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Linting
uses: snakemake/[email protected]
with:
directory: .
snakefile: ./workflow/Snakefile
args: "--lint --config ashleys_pipeline=True"
Testing_ashleys:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Testing data
uses: snakemake/[email protected]
with:
directory: .
snakefile: ./workflow/Snakefile
stagein: "conda config --set channel_priority flexible"
args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --conda-frontend mamba -p --verbose --debug"
- name: Testing report
uses: snakemake/[email protected]
with:
directory: .
snakefile: ./workflow/Snakefile
args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --conda-frontend mamba --report report.zip"
Testing_ashleys_fastqc_enabled:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Testing data
uses: snakemake/[email protected]
with:
directory: .
snakefile: ./workflow/Snakefile
stagein: "conda config --set channel_priority flexible"
args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config MultiQC=True --conda-frontend mamba -p --verbose --debug"
- name: Testing report
uses: snakemake/[email protected]
with:
directory: .
snakefile: ./workflow/Snakefile
args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config MultiQC=True --conda-frontend mamba --report report.zip"
Testing_ashleys_ms_norm_enabled:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Testing data
uses: snakemake/[email protected]
with:
directory: .
snakefile: ./workflow/Snakefile
stagein: "conda config --set channel_priority flexible"
args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config multistep_normalisation=True --conda-frontend mamba -p --verbose --debug"
- name: Testing report
uses: snakemake/[email protected]
with:
directory: .
snakefile: ./workflow/Snakefile
args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config multistep_normalisation=True --conda-frontend mamba --report report.zip"
Testing_ashleys_hg38:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Testing data
uses: snakemake/[email protected]
with:
directory: .
snakefile: ./workflow/Snakefile
stagein: "conda config --set channel_priority flexible"
args: "--cores 1 --use-conda --config reference=hg38 use_light_data=True chromosomes=[chr17] --conda-frontend mamba -p --verbose --debug"
- name: Testing report
uses: snakemake/[email protected]
with:
directory: .
snakefile: ./workflow/Snakefile
args: "--cores 1 --use-conda --config reference=hg38 use_light_data=True chromosomes=[chr17] --conda-frontend mamba --report report.zip"
Testing_ashleys_hg19:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Testing data
uses: snakemake/[email protected]
with:
directory: .
snakefile: ./workflow/Snakefile
stagein: "conda config --set channel_priority flexible"
args: "--cores 1 --use-conda --config reference=hg19 use_light_data=True chromosomes=[chr17] --conda-frontend mamba -p --verbose --debug"
- name: Testing report
uses: snakemake/[email protected]
with:
directory: .
snakefile: ./workflow/Snakefile
args: "--cores 1 --use-conda --config reference=hg19 use_light_data=True chromosomes=[chr17] --conda-frontend mamba --report report.zip"
Testing_ashleys_T2T:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Testing data
uses: snakemake/[email protected]
with:
directory: .
snakefile: ./workflow/Snakefile
stagein: "conda config --set channel_priority flexible"
args: "--cores 1 --use-conda --config reference=T2T use_light_data=True chromosomes=[chr17] --conda-frontend mamba -p --verbose --debug"
- name: Testing report
uses: snakemake/[email protected]
with:
directory: .
snakefile: ./workflow/Snakefile
args: "--cores 1 --use-conda --config reference=T2T use_light_data=True chromosomes=[chr17] --conda-frontend mamba --report report.zip"
Testing_ashleys_mm10:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Testing data
uses: snakemake/[email protected]
with:
directory: .
snakefile: ./workflow/Snakefile
stagein: "conda config --set channel_priority flexible"
args: "--cores 1 --use-conda --config reference=mm10 use_light_data=True chromosomes=[chr17] --conda-frontend mamba -p --verbose --debug"
- name: Testing report
uses: snakemake/[email protected]
with:
directory: .
snakefile: ./workflow/Snakefile
args: "--cores 1 --use-conda --config reference=mm10 use_light_data=True chromosomes=[chr17] --conda-frontend mamba --report report.zip"
Testing_jub_nb:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Testing data
uses: snakemake/[email protected]
with:
directory: .
snakefile: ./workflow/Snakefile
stagein: "conda config --set channel_priority flexible"
args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config hand_selection=True --conda-frontend mamba -p --verbose --debug"
- name: Testing report
uses: snakemake/[email protected]
with:
directory: .
snakefile: ./workflow/Snakefile
args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config hand_selection=True --conda-frontend mamba --report report.zip"
Testing_publishdir:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Testing data
uses: snakemake/[email protected]
with:
directory: .
snakefile: ./workflow/Snakefile
stagein: "conda config --set channel_priority flexible"
args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config publishdir=.tests/data_chr17_publishdir --conda-frontend mamba -p --verbose --debug"
- name: Testing report
uses: snakemake/[email protected]
with:
directory: .
snakefile: ./workflow/Snakefile
args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config publishdir=.tests/data_chr17_publishdir --conda-frontend mamba --report report.zip"
Testing_list_commands:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Testing data
uses: snakemake/[email protected]
with:
directory: .
snakefile: ./workflow/Snakefile
args: "--cores 1 --config list_commands=True --verbose --debug"