Ward D

rMats - summary

1

Include summary.py run after rMats invocation

mamba vs conda

1

given the default solver for conda is the libmamba solver since 23.10, one could think about dropping the mamba requirement

It seems pytests would require the use of ruamel yaml instead of pyyaml (#966) (at least if we want to keep generating all the data 'on the fly'). This seems...

CI dag test

1

Using -q / --quiet on top of a dryrun would make parsing the proposed number of rules more straight forward and easier to replicate with changing versions of snakemake. (which...

reformat print line to get rid off unwanted spaces

3

Hi, Thanks for the software ! I've noticed that the extract_snps script introduces spaces directly after the geno[1] field, at the position where the print line is split up over...

createIndices yaml output

1

By default the organism yaml gets written to the default organism folder (which makes sense). An additional copy in the actual output folder of the run would also be good...

set up pypi push action

makePairs workflow cleanup

1

- [ ] alignerThreads is set under config, but should respect predefined 'maxThreads' directives - [ ] non-fqc, but mainly alternative trimming modes are not tested and most likely do...

Some arguments should be removed or verified since 3.0, i.e.: - clusterConfig -> remove - maxJobs -> verify - .. ?

Internally reported: combine_loom rule doesn't properly create it's output dir, resulting in 'file not exists' error.