diff --git a/.github/workflows/filtering-ci.yml b/.github/workflows/filtering-ci.yml index b3236680..9dc06cad 100644 --- a/.github/workflows/filtering-ci.yml +++ b/.github/workflows/filtering-ci.yml @@ -57,13 +57,7 @@ jobs: - name: Preparing the data run: | mkdir -p teaseq/preprocessing && cd teaseq/preprocessing - # curl -L -o TODO https://figshare.com/ndownloader/files/TODO - - - name: Preparing the data (artifact) - uses: actions/download-artifact@v3 - with: - name: teaseq_unfilt.h5mu - path: teaseq/preprocessing/teaseq_unfilt.h5mu + # curl -L -o teaseq_unfilt.h5mu https://figshare.com/ndownloader/files/44639302 # Note: we run the following to test that the commands works # However, the following task will replacing the file anyway @@ -78,26 +72,26 @@ jobs: cd teaseq/preprocessing curl -o pipeline.yml https://panpipes-tutorials.readthedocs.io/en/latest/_downloads/efb55f083a8aeb1bc12f18ac61f6637b/pipeline.yml - # - name: Replace template contents in configuration file - # run: | - # cd teaseq/preprocessing - # sed -i 's+/Users/fabiola.curion/Documents/devel/miniconda3/envs/pipeline_env+pipeline_env+g' pipeline.yml + - name: Replace template contents in configuration file + run: | + cd teaseq/preprocessing + sed -i 's+/Users/fabiola.curion/Documents/devel/miniconda3/envs/pipeline_bbknn+pipeline_env+g' pipeline.yml - name: File tree if: env.debug == 'true' run: tree teaseq - # - name: Review pipeline tasks - # shell: bash -el {0} - # run: | - # cd teaseq/preprocessing - # panpipes preprocessing show full --local - - # - name: Run pipeline tasks - # shell: bash -el {0} - # run: | - # cd teaseq/preprocessing - # panpipes preprocessing make full --local + - name: Review pipeline tasks + shell: bash -el {0} + run: | + cd teaseq/preprocessing + panpipes preprocess show full --local + + - name: Run pipeline tasks + shell: bash -el {0} + run: | + cd teaseq/preprocessing + panpipes preprocess make full --local - name: File tree if: env.debug == 'true'