Ian Light-Maka
Ian Light-Maka
I think it would be good to have a module for [KrakenUniq](https://github.com/fbreitwieser/krakenuniq) - [x] This module does not exist yet with the [`nf-core modules list`](https://github.com/nf-core/tools#list-modules) command - [x] There is...
# nf-core/eager feature request Allow mapped reads to be converted to fastq for input into metagenomic screening steps. ## Is your feature request related to a problem? Please describe Lack...
TODOS: - [ ] Ensure files passed to metagenomics profiling are identifiable with outputted names (eg should be able to distinguish mapped, vs unmapped to ref (if user selects 'all':...
related to issue #1136 modern test conversion to dsl2 nf-test runtime 128.691s ## PR checklist - [x] This comment contains a description of changes (with reason). - [ ] If...
Aida mentioned that the default behavior of always collapsing libraries within a single sample for input into genotyping may be inappropriate when mutliple libs have different UDG treatment status/damage models,...
Main bulk of this adjustment relates to #1128. Otherwise, this is a QOL improvement/update for post mapping inputs into genotyping and its interactions with damage manipulation. Ascurrently implemented, this is...
Modules config entry for preloaded_krakenuniq is doubled, and inconsistent. confirm expected behavior to be consistent across profiling pipelines and remove redundant module config entry.
## Description of the bug The [reduced size human bam file]( https://github.com/nf-core/test-datasets/blob/eager/testdata/Human/bam/JK2067.bam) (Ch21-X) still has the @SQ tags for all contigs on the human reference genome. This causes issues for...