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Add support pipeline test extra flags #102

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merged 3 commits into from
May 27, 2024
Merged

Add support pipeline test extra flags #102

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fa4755d
Add support for extra pipeline flags
endast May 27, 2024
3199478
Test extra flag
endast May 27, 2024
8ae0c51
Revert "Test extra flag"
endast May 27, 2024
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5 changes: 4 additions & 1 deletion .github/workflows/run-pipeline.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,9 @@ on:
pipeline_file:
required: true
type: string
pipeline_extra_flags:
required: false
type: string
no_gpu:
required: false
type: boolean
Expand Down Expand Up @@ -79,7 +82,7 @@ jobs:
python -m snakemake ${{ (inputs.dry_run && '-n') || '' }} \
-j 2 --directory ${{inputs.pipeline_directory}} \
${{ (endsWith(inputs.pipeline_config, 'ml') && '--configfile') || '' }} ${{ inputs.pipeline_config }} \
--snakefile ${{inputs.pipeline_file}} --show-failed-logs -F
--snakefile ${{inputs.pipeline_file}} --show-failed-logs -F ${{ inputs.pipeline_extra_flags }}
shell: micromamba-shell {0}
- name: Run post pipeline cmd
if: inputs.postrun_cmd
Expand Down