Thiseas C. Lamnidis
Thiseas C. Lamnidis
### Is there an existing module for this? - [X] I have searched for the existing module ### Is there an open PR for this? - [X] I have searched...
Add module for eigenstratdatabsetools/snpcoverage. ## PR checklist Closes #853 - [x] This comment contains a description of changes (with reason). - [x] If you've fixed a bug or added code...
### Description of feature The latest template removed the libs directory, and moved any pipeline-specific functions into `subworkflows/local/utils_nfcore_eager_pipeline/main` (example from eager). Now, we include these in the include block in...
Closes #987 ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should...
It would be nice to either swap to CRAM files, or offer that as an option.
Currently, the eager documentation defines Mt/nuc ratio as > **MT to Nuclear Ratio This from MTtoNucRatio.** This reports the number of reads aligned to a mitochondrial entry in your reference...
See https://github.com/stschiff/sequenceTools/issues/24 In cases where PE un-collapsed reads from a single-stranded library are used in pileupcaller, the damage model is off, and damage artefacts will still make it into the...
Release 2.5.0 saw updates to the information added to RG tags when mapping reads through nf-core/eager. These updates should be mirrored in the reimplementation in DSL2. > Updated RG tags...
The print nuclear contaminatino script produces a JSON with the results, in which the `na` value is set to `"N/A"`. This should be replaced with a valid JSON missing value...
When bam input conversion to fastQ is added for remapping, ensure that lane information is kept in the output file names to avoid file name collisions