convert shell commands to snakemake wrappers

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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convert shell commands to snakemake wrappers #1

Closed sanjaynagi closed 3 years ago

sanjaynagi commented 4 years ago

For reproducibility, we need to convert shell commands to wrappers where they exist.

sanjaynagi commented 3 years ago

Mostly complete, but not fully tested yet. SnpEff had to use local version (v5.0) as version 4.5 on conda has problems downloading certain dbs, including aedes aegypti

sanjaynagi commented 3 years ago

[X] Kallisto index and quant tested, working
[ ] Freebayes, HISAT2, samtools need testing

sanjaynagi commented 3 years ago

just freebayes atm left to do. SnpEff when version 4.3.1 is updated to 5.0 on conda

sanjaynagi commented 3 years ago

SnpEff v5.0 now on conda. freebayes could still be converted to wrapper but closing for now