eager
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nf-core
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
## Feature description Upload of the wrong things to the ENA is a common and deeply frustrating phenomenon in the field. Noone is above it. It would be nice if...
On March 31st, we decided to make the publication of all large output files that are used for down-stream processing, particularly bam files after mapping, etc., opt-in.
HapCon is an autosomal contamination estimator packaged with hapROH. Already on conda.
Because evenness of coverage s a useful authentication step
As discussed ```[tasklist] ### Tasks - [ ] https://github.com/nf-core/eager/issues/999 ```
Now that we separated damage estimation and manipulation, PMDTools would need to be ran twice potentially, once for PMD Filtering and once as a damage estimation tool (if so chosen...
Merges happen at these levels: - pairness (BAMs are always SE, so that should be fine.) - lane - udg - library_id
When users provide multiple BAM files from the same library as BAM input for nf-core/eager, the only attribute that can be different between rows (other than the BAM path) is...
Currently, nf-core/eager does only allow to extract reads that didn't align to the provided reference genome into a single FastQ file. While this is no issue when having merged overlapping...
Due to issue here: https://github.com/nextflow-io/nextflow/issues/2662 Only affects DSL2 pipelines, thus does not affect eager2 but WILL apply to eager3