r-base to 3.6, default off (spia, fgsea, goatools), fix sleuth RAM problem

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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Closed dlaehnemann closed 5 years ago

dlaehnemann commented 5 years ago

r-base = 3.6 in all environments
introduce activate: false defaults for spia, fgsea and goatools (set to true to run the tools)
restrict thread usage of sleuth_prep() in rule sleuth_init to whatever the pipeline provides (with a current default max at 6), instead of letting it take whatever it can find -- this can lead to high RAM usage and running R code in the form of scripts seems to have a hard limit at 40 GB RAM

dlaehnemann commented 5 years ago

@johanneskoester this passes, a review of the changes would be very much appreciated.