M Bernt
so we need to copy it FOR CONTRIBUTOR: * [x] - I have read the [CONTRIBUTING.md](https://github.com/galaxyproject/tools-iuc/blob/master/CONTRIBUTING.md) document and this tool is appropriate for the tools-iuc repo. * [x] - License...
With https://github.com/galaxyproject/planemo/pull/1190 its possible to detect tools that write to Galaxy's files directory. I'm running this on IUC here: https://github.com/bernt-matthias/tools-iuc/runs/3721212988?check_suite_focus=true See also discussion in https://github.com/galaxyproject/tools-iuc/pull/3986#issuecomment-926729276 Here is a list of...
if not set the roadmap files (and assemblies?) differ when using different numbers of cores see also https://www.biostars.org/p/86907/ .. does not work for 1 CPU https://github.com/dzerbino/velvet/issues/56 FOR CONTRIBUTOR: * [x]...
The options filter seems to be evaluated on tool load https://github.com/galaxyproject/tools-iuc/blob/b991ebbd9f59ffff1b3eae09f65b59b02ad7cf8e/tools/mitos/mitos.xml#L47 which slows down tool loading for large histories / collections Maybe replace by validator
Currently there are 3 data data tables: - bwa_mem_indexes - bwa_mem2_indexes - bwameth_indexes where the second has apparently no data manager. Since version 0.2.3 bwameth also supports bwa_mem2 indices. The...
Seems to me that the databases are currently stored next to the library. This does not work for read-only installations (e.g. containers and multi user installations) and is considered bad...
#### Is your feature request related to a problem? Please specify. 1. When using `mapper | samtools sort - ` it is difficult to specify the number of threads for...
bedSort outputs the following for the SNPs dataset from UCSC ``` ... chr22 17586594 17586595 rs34484815 0 + chr22 17586605 17586605 rs536619616 0 + chr22 17586604 17586605 rs560126106 0 +...
I noticed that the CLI help mentions different sets of operations for different tools. For instance groupby has absmin, but merge not... Or can I assume that the operations defined...
For using Nanoplot in workflows it would be handy if the presence of `NanoStats_post_filtering.txt` would be predictable from the command line parameters, i.e. independent if anything was filtered. Currently one...