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fix: just switch to html github md not rendering #159

fix: just switch to html github md not rendering

fix: just switch to html github md not rendering #159

Workflow file for this run

name: Dry Runs
on:
push:
jobs:
dry_run_paired_end:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
with:
submodules: 'true'
- uses: docker://snakemake/snakemake:v7.32.4
- name: Dry Run with test data
run: |
docker run -h cn0000 -v $PWD:/opt2 -w /opt2 snakemake/snakemake:v7.32.4 /bin/bash -c \
"source get_submods.sh; pip install -r requirements.txt; ./weave run --sheetname paired_end.csv -s /opt2/.tests/paired_end -o /opt2/.tests/dry_run_out --local --dry-run /opt2/.tests/paired_end"
- name: View the pipeline config file
run: |
echo "Generated config file for pipeline...." && cat $PWD/.tests/dry_run_out/paired_end/.config/config_job_0.json
- name: Lint Snakefile
continue-on-error: true
run: |
docker run -e SNK_CONFIG='/opt2/.tests/dry_run_out/paired_end/.config/config_job_0.json' -v $PWD:/opt2 snakemake/snakemake:stable snakemake --lint -s /opt2/workflow/Snakefile -d /opt2/workflow || \
echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.'
dry_run_latest:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
with:
submodules: 'true'
- uses: docker://snakemake/snakemake:stable
- name: Dry Run with test data
run: |
docker run -h cn0000 -v $PWD:/opt2 -w /opt2 snakemake/snakemake:stable /bin/bash -c \
"source get_submods.sh; pip install -r requirements.txt; ./weave run --sheetname paired_end.csv -s /opt2/.tests/paired_end -o /opt2/.tests/dry_run_out --local --dry-run /opt2/.tests/paired_end"
- name: View the pipeline config file
run: |
echo "Generated config file for pipeline...." && cat $PWD/.tests/dry_run_out/paired_end/.config/config_job_0.json
- name: Lint Snakefile
continue-on-error: true
run: |
docker run -e SNK_CONFIG='/opt2/.tests/dry_run_out/paired_end/.config/config_job_0.json' -v $PWD:/opt2 snakemake/snakemake:stable snakemake --lint -s /opt2/workflow/Snakefile -d /opt2/workflow || \
echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.'
dry_run_single_end:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
with:
submodules: 'true'
- uses: docker://snakemake/snakemake:v7.32.4
- name: Dry Run with test data
run: |
docker run -h cn0000 -v $PWD:/opt2 -w /opt2 snakemake/snakemake:v7.32.4 /bin/bash -c \
"source get_submods.sh; pip install -r requirements.txt;./weave run --sheetname single_end.csv -s /opt2/.tests/single_end -o /opt2/.tests/dry_run_out --local --dry-run /opt2/.tests/single_end"
- name: View the pipeline config file
run: |
echo "Generated config file for pipeline...." && cat $PWD/.tests/dry_run_out/single_end/.config/config_job_0.json
- name: Lint Snakefile
continue-on-error: true
run: |
docker run -e SNK_CONFIG='/opt2/.tests/dry_run_out/single_end/.config/config_job_0.json' -v $PWD:/opt2 snakemake/snakemake:stable snakemake --lint -s /opt2/workflow/Snakefile -d /opt2/workflow || \
echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.'