Thiseas C. Lamnidis

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...

## 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...

HapCon is an autosomal contamination estimator packaged with hapROH. Already on conda.

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...

DSL2: Add test profile that forces ALL the possible merging steps for FastQ and BAM inputs, to ensure no file name collisions happen.

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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...

Add Yleaf to PyPI/bioconda

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Are there plans to add Yleaf to PyPI and/or bioconda? (I did not find it on either. Sorry if it is already there.) The existing conda environment file is already...

Best for publishDir to be explicitly on/off, and all modules (even when not publishing) need an ext.prefix, now that we don't have meta.id anymore. Also ensure that all module configurations...

Use Sample-level merged BAMs for sample-level statistics

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Qualimap needs an `ext.prefix`. Additionally, Qualimap results are meant to be at the sample level, but are currently at the Library level. We need to use post-Library-merge BAMs as input...

When running DamageProfiler (`0.4.9`, within nf-core/eager `2.4.6`) on larger bam files, the rate at which reads are processed becomes slower and slower. At first: ``` 2023-07-28 12:12:04 INFO StartCalculations:115 -...