Make both Gene and isoform DE optional + fix for .xlsx, .csv metadata

sanjaynagi / rna-seq-pop

Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data

https://sanjaynagi.github.io/rna-seq-pop/

MIT License

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Closed sanjaynagi closed 1 year ago

sanjaynagi commented 1 year ago

In this PR we make #88 isoform DE optional. It's conda env is not currently working on Neptune.

We also fix for .xlsx and .csv metadata usage - forgot to edit common.smk and progressiveGenes.py and generateFreebayesParams.R
We also fix the karyotype notebook argument parsing (reads config instead)