fix tests for workflow created from template

snakemake-workflows / rna-seq-kallisto-sleuth

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

MIT License

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fix tests for workflow created from template #9

Closed dlaehnemann closed 4 years ago

dlaehnemann commented 4 years ago

Creating a workflow via the template does not include the submodule with ngs-test-data and results in the automatic GitHub Actions tests failing. This pull-request reverts folder naming (especially in units.tsv) to the default naming when adding the ngs-test-data submodule and includes instructions on how to do that for a newly template-generated workflow in the README.md's section on testing.

dlaehnemann commented 4 years ago

This finally passes, with a major change to how bioconductor species packages for R are handled. This does feel like a hacky workaround, but it avoids using biomart for stuff that we need in multiple anyways. But @johanneskoester , please have a thorough look!

dlaehnemann commented 4 years ago

Bump @johanneskoester for a review...

dlaehnemann commented 4 years ago

Bump @johanneskoester for a review. This seems to now be in conflict with some of the spia changes you implemented. At the same time, it might be a fix to the Issues #11 and #8 , so probably worth merging soon.