Johannes Köster issues

Results 62 issues of


Johannes Köster

Roadmap / Todos

This is a continuously updated list of Todos. If you have a suggestion, comment to the issue. We will update the list if the suggestion fits in. Please note that...

fix: lexicographically sorted rule display with --list, and trimmed rule docstrings

### QC * [x] The PR contains a test case for the changes or the changes are already covered by an existing test case. * [x] The documentation (`docs/`) is...

fix: delay evaluation of tmpdir to actual job execution, and not submission. This way, tmpdir can be dependent on the node context.

### Description see title ### QC * [x] The PR contains a test case for the changes or the changes are already covered by an existing test case. * [x]...

feat: allow for human friendly resource definitions (e.g. mem="5GB", runtime="1d")

### Description ### QC * [ ] The PR contains a test case for the changes or the changes are already covered by an existing test case. * [ ]...

Provide LPMX as a conda package

It would be nice if LPMX could be installed via Conda, by hosting a package on conda-forge. I am unsure in what way this statement here will make this hard:...

feat: add initial support for arm builds

Support for arm builds (macos-M1 and linux-graviton) via CircleCI. # TODOs * [x] Merge aarch64 support in bioconda-utils: https://github.com/bioconda/bioconda-utils/pull/866 * [x] Support for downloading artifacts from CircleCI. This needs to...

WIP

feat: allow definition of access pattern for input files

### Description ### QC * [ ] The PR contains a test case for the changes or the changes are already covered by an existing test case. * [ ]...

fix: register vcfstreamsort for linking against libwfa.

hopefully fixes #389. CUrrently testing the same fix as a patch on bioconda: https://github.com/bioconda/bioconda-recipes/pull/42673

Transfer ownership of Snakemake tibanna plugin

As you might have heard, the upcoming Snakemake 8.0 will get support for execution backend plugins (https://github.com/snakemake/snakemake/issues/2409). I have therefore moved the tibanna executor of Snakemake, which was originally developed...