search

snakemake-workflows / rna-seq-star-deseq2

RNA-seq workflow using STAR and DESeq2
MIT License
327 stars 203 forks source link

Updated all wrappers to most current version #59

Closed isaacvock closed 1 year ago

isaacvock commented 1 year ago

As a fix to the bug discussed in #58, I have updated all wrappers to the most up-to-date version (v.1.21.4).

dlaehnemann commented 1 year ago

The formatting failure seems to be an unrelated problem on the GitHub Actions tests. The GitHub Action to check out submodules has been deprecated: https://github.com/textbook/git-checkout-submodule-action/commit/29d40a332e161d7cb51fea5f3c8dd15ff6edbc31

dlaehnemann commented 1 year ago

@isaacvock : Is it OK if I further hijack your PR to fix more stuff? It seems like we are now running into trouble with the new channel_priority: strict in conda or something similar, so it would probably make sense to also update and fix all the workflow/envs/*.yaml files...

isaacvock commented 1 year ago

Error in most recent tests indicated that output files for align rule were expected to have specific named attributes. Checking the wrapper code seems to indicate that alignment bam/sam needs to be explicitly assigned the attribute "aln" and the reads per gene output the attribute "reads_per_gene". Therefore, I added this to the align rule.

dlaehnemann commented 1 year ago

Yeah, these are the little kinds of changes that are to be expected...

isaacvock commented 1 year ago

This time I think the problem was that they changed the expected name of the index attribute from index to idx, I changed it accordingly in the params block.

dlaehnemann commented 1 year ago

Many thanks for playing along...

whack-a-mole