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snakemake-workflows / rna-seq-kallisto-sleuth

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
MIT License
66 stars 44 forks source link

perf: datavzrd wrapper `v3.12.1`, offer-excel configurable, free disk space for CI, dynamic sleuth_init mem_mb, pure download rules as localrules #92

Closed dlaehnemann closed 4 months ago

dlaehnemann commented 6 months ago

this then uses datavzrd=2.36.10

dlaehnemann commented 5 months ago

For now, I'll turn off the reactivated testing of isoformSwitchAnalyzer, to get the tests to pass here and merge this PR.

And then, I'll fix isoformSwitchAnalyzer on a new branch, where we'll also fix the Ensembl cDNA fasta file, as the current failure is due to the Ensembl GTF and the Ensembl cDNA FASTA file being out of sync, see here: https://www.r-bloggers.com/2020/01/comparing-ensembl-gtf-and-cdna/

Removing Ensembl cDNA FASTA redundancies (the same HGNC gene symbol appearing with multiple Ensembl gene_ids due to scaffolds and other issues), will probably remove most of the FASTA-only transcript IDs as well, so should be part of the isoformSwitchAnalyzer fix...

fxwiegand commented 5 months ago

It would probably also makes sense to upgrade to 2.36.15 as this will probably save loads of space in the resulting reports 😊