Data availability?

[Vanessasaurus]

Hi! I'm using this as a test workflow for an orchestration tool, and I'm not familiar with the workflow itself and am looking for some dummy data so this doesn't happen:

Building DAG of jobs...
MissingInputException in rule align  in line 1 of https://github.com/snakemake-workflows/rna-seq-star-deseq2/raw/v1.2.0/workflow/rules/align.smk:
Missing input files for rule align:
    output: results/star/A-lane1/Aligned.sortedByCoord.out.bam, results/star/A-lane1/ReadsPerGene.out.tab
    wildcards: sample=A, unit=lane1
    affected files:
        A.2.fq.gz
        A.1.fq.gz

Is this readily available, and if not, is there another workflow in the catalog with data that is (maybe beyond the basic Snakemake getting started workflow?) Thank you!

[David Laehnemann]

In the https://github.com/snakemake-workflows, we usually try to have basic test data in the .test/ directory in the main folder of the repo. Here, this is in the folder .test/ngs-test-data/reads/.

These are then used during GitHub Actions continuous integration testing. For this workflow, see here for the tests that are run:

rna-seq-star-deseq2/.github/workflows/main.yml

Lines 35 to 56 in dfd0b9c

 run-workflow: 
   runs-on: ubuntu-latest 
   needs: 
     - linting 
     - formatting 
   steps: 
   - name: Checkout repository 
     uses: actions/checkout@v1 
   - name: Checkout submodules 
     uses: textbook/git-checkout-submodule-action@2.0.0 
   - name: Test workflow 
     uses: snakemake/snakemake-github-action@v1.22.0 
     with: 
       directory: .test 
       snakefile: workflow/Snakefile 
       args: "--use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache" 
   - name: Test report 
     uses: snakemake/snakemake-github-action@v1.22.0 
     with: 
       directory: .test 
       snakefile: workflow/Snakefile 
       args: "--report report.zip" 

Does this help?

[Vanessasaurus]

Yes that's perfect! I totally glossed over the test directory, thanks for the helpful reminder.