eager
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nf-core
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
**Is your feature request related to a problem? Please describe.** In some cases, a user may want to know if there is any differences in terms of gene functionality/expression. One...
In some metagenomic contexts, there can be closely related species in a sample that can make read mapping to a single reference genome difficult (e.g. cross-mapping of reads between species)....
We should have the possibility to output CRAM files
We could think about splitting BAMs as DeDup/MarkDup takes quite some time normally and use a `file.size>2GB` (or similar operator) to speed up things significantly. A subsequent merge would be...
A bunch of aDNA-aware genotypers have been released relatively recently. We should add these as possible options Here is a running list: - [ ] snpAD: https://bioinf.eva.mpg.de/snpAD/ - [ ]...
Me again 😁 I already really appreciate that genotyping with pileupCaller as implemented in eager2 works for both single- and double-stranded libraries in the same run, creating two genotypes. The...
**Is your feature request related to a problem? Please describe.** @pontussk suggests including the possibility for users to run PMDtools with the following flag [`--platypus`](https://github.com/pontussk/PMDtools/blob/1b0aa0592edb3e6ae1f0f2ca705e6ffbdedb2d8d/pmdtools.0.60.py#L100). This is apparently used for...
See here : https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-07229-y
Start adding FASTP/ADAPTERREMOVAL subworkflwos ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code...
- FASTQC - FASTP/ADAPTERREMOVAL - FASTQC POST - BWA ALN/BWA MEM/BOWTIE2/CIRCULAR MAPPING ## Indexing - BWA INDEX / BOWTIE2 INDEX (https://github.com/nf-core/eager/pull/926) / CIRCULARMAPPER - SAMTOOLS FAIDX - PICARD CREATESEQUENCEDICTIONARY ##...