eager
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nf-core
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
DSL2: Ensure to document input run BAMs will _not_ be merged with FASTQ libraries even if same name
Must either confvert to FASTQ and remap, or do manually outside
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...
This is important for read group tags, as it influences genotyping models. eager1/eager2 hardcoded illumina, which is not yet valid anymore due to rising use of MGI sequencers (as previously...
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
Allow users to configure bwa mem `-k` and `-r` parameters. ## Is your feature request related to a problem? Please describe ## Describe the solution you'd like ## Describe alternatives...