David Laehnemann

There is a similar list from last summer, which lacks some of the tools presented here, but also has some more. Maybe worth having a look at and integrating here?...

This is a follow-up feature request to issue #85 that deals with comment formatting. Handling of [one of the test cases there](https://github.com/snakemake/snakefmt/issues/85#issuecomment-730275169), with aligned comments across multiple lines to hide...

consistently distinguish mapq (mapping quality) from qual (base calling error probabilities)

2

This came up in issue #795, opening it here to keep it documented beyond the closing of that issue: It is confusing when reading the code, that the mapping quality...

### Description This is a first attempt, will update with a tmp-folder based solution in a bit. ### QC For all wrappers added by this PR, I made sure that...

separate contribution section describing writing of `wrapper.(py|R)`

1

The contribution docs are currently being extended and improved by @mbhall88 in PR #380. During the review of this process, we re-identified a long standing shortcoming of the contribution docs,...

utility functions for general-purpose wrapper setup (e.g. JVM memory option handling)

1

**Is your feature request related to a problem? Please describe.** @tdayris is currently working on unifying the handling of Java memory specifications in wrappers where the bioconda recipes allow for...

use `resources: mem_gb=3` specs in all Java tools to request `-Xmx{snakemake.resources.mem_gb}G`

4

**Is your feature request related to a problem? Please describe.** Specifying this via `params` strings makes snakemake unaware of these resources. **Describe the solution you'd like** Via `resources`, snakemake can...

fix double-negation in gene_column check upon manual change of pval_aggregate in sleuth_object

1

The changed code would previously stop with an error, if you assigned the value `TRUE` to `pval_aggregate` in a sleuth object with the `gene_column` defined, contrary to the error message...

add support for other model file formats than `.lp` (e.g. the `MPS` format)

5

Issues #73 and #72 demonstrate that the `.lp` file format is not very clearly specified. It might thus be more stable to use other more clearly file formats for any...

merge samples in kallisto_quant step

2

This PR implements sample merging by providing kallisto with all the units of a sample at once. I.e. if multiple sequencing runs are provided for a sample as units, kallisto...