From fa4755de4aad8093299235c58b9bcc545e4f14c7 Mon Sep 17 00:00:00 2001 From: Magnus Wahlberg Date: Mon, 27 May 2024 10:53:51 +0200 Subject: [PATCH 1/3] Add support for extra pipeline flags --- .github/workflows/run-pipeline.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/run-pipeline.yml b/.github/workflows/run-pipeline.yml index 6971a7fd..47f02e8b 100644 --- a/.github/workflows/run-pipeline.yml +++ b/.github/workflows/run-pipeline.yml @@ -12,6 +12,9 @@ on: pipeline_file: required: true type: string + pipeline_extra_flags: + required: false + type: string no_gpu: required: false type: boolean @@ -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 From 31994789be4ca882824f776f9fcd43680b17dcce Mon Sep 17 00:00:00 2001 From: Magnus Wahlberg Date: Mon, 27 May 2024 10:55:59 +0200 Subject: [PATCH 2/3] Test extra flag --- .github/workflows/pipeline-tests.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/pipeline-tests.yml b/.github/workflows/pipeline-tests.yml index 0cf7e64c..66d70dbb 100644 --- a/.github/workflows/pipeline-tests.yml +++ b/.github/workflows/pipeline-tests.yml @@ -9,6 +9,7 @@ jobs: with: pipeline_file: ./pipelines/run_training.snakefile environment_file: ./deeprvat_env_no_gpu.yml + pipeline_extra_flags: --verbose Pipeline-Tests-RunTraining: needs: Smoke-RunTraining From 8ae0c51971926804cb0b5795db391a79ad2f0c74 Mon Sep 17 00:00:00 2001 From: Magnus Wahlberg Date: Mon, 27 May 2024 11:00:41 +0200 Subject: [PATCH 3/3] Revert "Test extra flag" This reverts commit 31994789be4ca882824f776f9fcd43680b17dcce. --- .github/workflows/pipeline-tests.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/pipeline-tests.yml b/.github/workflows/pipeline-tests.yml index 66d70dbb..0cf7e64c 100644 --- a/.github/workflows/pipeline-tests.yml +++ b/.github/workflows/pipeline-tests.yml @@ -9,7 +9,6 @@ jobs: with: pipeline_file: ./pipelines/run_training.snakefile environment_file: ./deeprvat_env_no_gpu.yml - pipeline_extra_flags: --verbose Pipeline-Tests-RunTraining: needs: Smoke-RunTraining