Thiseas C. Lamnidis

Add an option to subsample the input

1

Currently, there is no way to randomly subsample an input bam within DamageProfiler. When the input bams are very large, this can increase the runtime considerably, while the damage rates...

Add KIN

3

Adds [KIN](https://github.com/DivyaratanPopli/Kinship_Inference) ---- Please read the [guidelines for Bioconda recipes](https://bioconda.github.io/contributor/guidelines.html) before opening a pull request (PR). ### General instructions * If this PR adds or updates a recipe, use "Add"...

Adding r-bootsvd recipe from conda_r_skeleton_helper

3

Recipe made using https://github.com/bgruening/conda_r_skeleton_helper Checklist - [x] Title of this PR is meaningful: e.g. "Adding my_nifty_package", not "updated meta.yaml". - [x] License file is packaged (see [here](https://github.com/conda-forge/staged-recipes/blob/5eddbd7fc9d1502169089da06c3688d9759be978/recipes/example/meta.yaml#L64-L73) for an example)....

DSL2: Genotyping on multiple snp sets in one run?

1

It might be nice to be able to genotype on multiple SNP sets in a single run. I'm specifically thinking of pileupcaller here, not sure how it would apply to...

add ENA prep profile This profile simply skips any skippable steps, and runs AR without any length/quality filtering and without merging reads.

DSL2: Options for different adapters for ssDNA and dsDNA libraries within the same run.

1

ssDNA libraries have a different R2 adapter than dsDNA libraries, meaning that processing both types of libraries together currently requires an adapterlist to be provided. Omission of the list leaves...

DSL2: Ensure that all sharded fastQs make it into mapping.

3

(Preface: I might be under caffeinated and seeing things, BUT) I think the sharded FastQs never actually make it to mapping? It looks like a channel `ch_input_for_mapping` is correctly created...

DSL2: Add bamRefine as a damage manipulation alternative?

1

https://www.biorxiv.org/content/10.1101/2023.11.11.566695v1

naming a snapshot section `mapping` omits it from the snapshot?

2

I am using `nft-utils` to collect a set of files from the output of my pipeline, and then test them for consistency in content or name using `nf-test`. Here's part...

**Describe the bug** https://nf-co.re/docs/nf-core-tools/ does not show `patch` as a subtools applicable to subworkflows, even though it does appear in the helptext when running `nf-core subworkflows` **To Reproduce** 1. Run...