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snakemake-workflows / rna-seq-star-deseq2

RNA-seq workflow using STAR and DESeq2
MIT License
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improve environment specifications #57

Closed mfansler closed 1 year ago

mfansler commented 1 year ago

The Bioconda specification is conda-forge > bioconda, so this corrects that. Additionally, all Bioconductor packages are tied to a single version of R. Explicitly specifying this in a YAML often improves solve times (especially noticeable for conda frontend).

dlaehnemann commented 1 year ago

Does the merging of #59 do the trick for you? I know it doesn't pin r-base, but I think solving times are not the most important bottle neck in these workflows (although I acknowledge that the wait on initial workflow runs can be annoying). In any case, feel free to open a new PR if you really want r-base pinned.

mfansler commented 1 year ago

That's fine - it was a "BTW" modification. Besides, I expect most Snakemake users are savvy enough to be using Mamba, which actually shows little-to-no gain with such optimizing constraints.

Also very happy to see more use of nodefaults! 👌