From b5c554941b5373a4982f1936a61aeb0274fc74d3 Mon Sep 17 00:00:00 2001 From: Kevin Rue-Albrecht Date: Mon, 5 Feb 2024 14:44:41 +0000 Subject: [PATCH] final setup and run --- .github/workflows/ingestion-ci.yml | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ingestion-ci.yml b/.github/workflows/ingestion-ci.yml index 98fb3ecd..cfdbdbe1 100644 --- a/.github/workflows/ingestion-ci.yml +++ b/.github/workflows/ingestion-ci.yml @@ -67,7 +67,21 @@ jobs: run: curl -o pipeline.yml https://panpipes-tutorials.readthedocs.io/en/latest/_downloads/9a4fcbc3c0a4fdc8e6578d086a88730f/pipeline.yml - name: Preparing the submission file - run: curl -o sample_file_qc.txt https://panpipes-tutorials.readthedocs.io/en/latest/_downloads/40ed291bf9a7ff73c4f396ec63cff2f7/sample_file_qc.txt + run: curl -o sample_file_qc.txt https://panpipes-tutorials.readthedocs.io/en/latest/_downloads/40ed291bf9a7ff73c4f396ec63cff2f7/sample_file_qc.txt + + - name: Preparing the QC gene lists + run: curl -o qc_genelist_1.0.csv https://panpipes-tutorials.readthedocs.io/en/latest/_downloads/fd38f25644105ea357a26e78a59139bb/qc_genelist_1.0.csv + + - name: Replace template contents in configuration file + run: sed 's+panpipes-tutorials/tutorials/ingesting_data/qc_genelist_1.0.csv+qc_genelist_1.0.csv+g' pipeline.yml + + - name: Review pipeline tasks + shell: bash -el {0} + run: panpipes ingest show full --local + + - name: Run pipeline tasks + shell: bash -el {0} + run: panpipes ingest make full --local - name: File tree if: env.debug == 'true'