From 9b99b283a152def9491704d62fd5a97ca1744d76 Mon Sep 17 00:00:00 2001 From: Magnus Wahlberg Date: Fri, 24 May 2024 12:15:46 +0200 Subject: [PATCH 1/8] Add postrun_cmd --- .github/workflows/run-pipeline.yml | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/.github/workflows/run-pipeline.yml b/.github/workflows/run-pipeline.yml index e5020d1d..e883d2dc 100644 --- a/.github/workflows/run-pipeline.yml +++ b/.github/workflows/run-pipeline.yml @@ -34,7 +34,13 @@ on: fasta_download_path: required: false type: string - + postrun_cmd: + required: false + type: string + postrun_shell: + required: false + type: string + default: bash -el # or micromamba-shell jobs: Run-Pipeline: runs-on: ubuntu-latest @@ -78,3 +84,7 @@ jobs: ${{ (endsWith(inputs.pipeline_config, 'ml') && '--configfile') || '' }} ${{ inputs.pipeline_config }} \ --snakefile ${{inputs.pipeline_file}} --show-failed-logs -F shell: micromamba-shell {0} + - name: Run post pipeline cmd + if: inputs.postrun_cmd + run: ${{inputs.postrun_cmd}} + shell: ${{ inputs.postrun_shell }} {0} From 0e6ef564178c9a8c1aeda3e54ba45c4e84ae0414 Mon Sep 17 00:00:00 2001 From: Magnus Wahlberg Date: Fri, 24 May 2024 12:18:07 +0200 Subject: [PATCH 2/8] test post run --- .github/workflows/pipeline-tests.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/pipeline-tests.yml b/.github/workflows/pipeline-tests.yml index 0cf7e64c..7997a054 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 + postrun_cmd: echo "Hello World from post" Pipeline-Tests-RunTraining: needs: Smoke-RunTraining @@ -17,7 +18,9 @@ jobs: pipeline_file: ./pipelines/run_training.snakefile environment_file: ./deeprvat_env_no_gpu.yml dry_run: false - + postrun_cmd: python --version + postrun_shell: micromamba-shell + # Association Testing Pretrained Pipeline Smoke-Association-Testing-Pretrained: uses: ./.github/workflows/run-pipeline.yml From 48dd557c631de26ee482fa7e8b4d21522b95ecaa Mon Sep 17 00:00:00 2001 From: Magnus Wahlberg Date: Fri, 24 May 2024 12:21:53 +0200 Subject: [PATCH 3/8] Update run-pipeline.yml --- .github/workflows/run-pipeline.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run-pipeline.yml b/.github/workflows/run-pipeline.yml index e883d2dc..1503031b 100644 --- a/.github/workflows/run-pipeline.yml +++ b/.github/workflows/run-pipeline.yml @@ -40,7 +40,7 @@ on: postrun_shell: required: false type: string - default: bash -el # or micromamba-shell + default: "bash -el" # or micromamba-shell jobs: Run-Pipeline: runs-on: ubuntu-latest From c05153b3d4fba31b11e4417dd6323f144820afdb Mon Sep 17 00:00:00 2001 From: Magnus Wahlberg Date: Fri, 24 May 2024 13:23:28 +0200 Subject: [PATCH 4/8] Update run-pipeline.yml --- .github/workflows/run-pipeline.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run-pipeline.yml b/.github/workflows/run-pipeline.yml index 1503031b..e883d2dc 100644 --- a/.github/workflows/run-pipeline.yml +++ b/.github/workflows/run-pipeline.yml @@ -40,7 +40,7 @@ on: postrun_shell: required: false type: string - default: "bash -el" # or micromamba-shell + default: bash -el # or micromamba-shell jobs: Run-Pipeline: runs-on: ubuntu-latest From 3f5558d5ff886d6355ce03197a36143d7b4ac1e9 Mon Sep 17 00:00:00 2001 From: Magnus Wahlberg Date: Fri, 24 May 2024 13:30:56 +0200 Subject: [PATCH 5/8] Update run-pipeline.yml --- .github/workflows/run-pipeline.yml | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/.github/workflows/run-pipeline.yml b/.github/workflows/run-pipeline.yml index e883d2dc..6971a7fd 100644 --- a/.github/workflows/run-pipeline.yml +++ b/.github/workflows/run-pipeline.yml @@ -37,10 +37,7 @@ on: postrun_cmd: required: false type: string - postrun_shell: - required: false - type: string - default: bash -el # or micromamba-shell + jobs: Run-Pipeline: runs-on: ubuntu-latest @@ -87,4 +84,4 @@ jobs: - name: Run post pipeline cmd if: inputs.postrun_cmd run: ${{inputs.postrun_cmd}} - shell: ${{ inputs.postrun_shell }} {0} + shell: micromamba-shell {0} From 140decdfd6c98c6ef784128e57ff18da544ac8b2 Mon Sep 17 00:00:00 2001 From: Magnus Wahlberg Date: Fri, 24 May 2024 13:31:29 +0200 Subject: [PATCH 6/8] Update pipeline-tests.yml --- .github/workflows/pipeline-tests.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/pipeline-tests.yml b/.github/workflows/pipeline-tests.yml index 7997a054..14dbd5b6 100644 --- a/.github/workflows/pipeline-tests.yml +++ b/.github/workflows/pipeline-tests.yml @@ -19,8 +19,7 @@ jobs: environment_file: ./deeprvat_env_no_gpu.yml dry_run: false postrun_cmd: python --version - postrun_shell: micromamba-shell - + # Association Testing Pretrained Pipeline Smoke-Association-Testing-Pretrained: uses: ./.github/workflows/run-pipeline.yml From 23889efbcaddbabb47b5ba7fcfbd41c0b59dc311 Mon Sep 17 00:00:00 2001 From: Magnus Wahlberg Date: Fri, 24 May 2024 13:36:20 +0200 Subject: [PATCH 7/8] Update pipeline-tests.yml --- .github/workflows/pipeline-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pipeline-tests.yml b/.github/workflows/pipeline-tests.yml index 14dbd5b6..d81d938b 100644 --- a/.github/workflows/pipeline-tests.yml +++ b/.github/workflows/pipeline-tests.yml @@ -9,7 +9,7 @@ jobs: with: pipeline_file: ./pipelines/run_training.snakefile environment_file: ./deeprvat_env_no_gpu.yml - postrun_cmd: echo "Hello World from post" + postrun_cmd: echo "Hi this should fail!" && exit 1 Pipeline-Tests-RunTraining: needs: Smoke-RunTraining From 2f450cd2928b6fd6fa0b647658e972875ac08c56 Mon Sep 17 00:00:00 2001 From: Magnus Wahlberg Date: Fri, 24 May 2024 13:37:20 +0200 Subject: [PATCH 8/8] Remove samples --- .github/workflows/pipeline-tests.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/pipeline-tests.yml b/.github/workflows/pipeline-tests.yml index d81d938b..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 - postrun_cmd: echo "Hi this should fail!" && exit 1 Pipeline-Tests-RunTraining: needs: Smoke-RunTraining @@ -18,7 +17,6 @@ jobs: pipeline_file: ./pipelines/run_training.snakefile environment_file: ./deeprvat_env_no_gpu.yml dry_run: false - postrun_cmd: python --version # Association Testing Pretrained Pipeline Smoke-Association-Testing-Pretrained: