Tessa Pierce Ward

... and add to bioconda-recipes!

combine units prior to khmer

8

k-mer trimming and diginorm should happen on the full `sample`, not each `sample-unit` pair of files. We now have a function to do this (currently in the salmon rule) that...

& output table of counts after tximport step. Useful for alternate DE, viz programs

https://github.com/dib-lab/eelpond/blob/0d0d22ccd9f8e3a57c9d09c4abed4c39c965f341/rules/deseq2/deseq2-env.yaml#L7 Useful: https://github.com/bioconda/bioconda-recipes/issues/13774#issue-413862378

related to https://github.com/dib-lab/dammit/issues/114 https://gist.github.com/ACharbonneau/45624bd5b6168267ba051da6802dd548

improve print_workflows option

2

`./run_eelpond -w` instead of `./run_eelpond nema-test -w`

- DESeq2 only works with replicates -- check sample replicate info before attempting the deseq2 workflow. - Add edgeR rule for no-replicate analysis.

`--forcetargets` doesn't always work as desired. Particularly for steps with intermediate targets that are not passed as `targets` to snakemake (e.g. dammit)

citation printing

1

1. build a `yaml` of program: citation(s) 2. enable a `--citation` option with workflows that will print all citations for that workflow to `stdout` or to a file. 3. also...

sharing issue arising from troubleshooting with @jeanzzhao **tl;dr:** Grist initial read processing is (silently) incorrect for samples that use `.1` or `.2` in read names (we assume this is used...