Dsl1 2.5.0

[TCLamnidis]

• Added option to use MapDamage instead of DamageProfiler for damage estimation. Also added options to downsample to a specified number of reads for damage calculation with mapDamage.
• Fixed a niche error causing file name collisons.

Closes #1020.
Closes #1017.
Clsoes #1031.

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - add to the software_versions process and a regex to scrape_software_versions.py
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/eager branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint .).
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[TCLamnidis]

still need:

• Mapdamage MultiQC module
• Final updates to output.md
• pass mapdamage stuff to MultiQC

[jfy133]

Needs adding of mapDamage to README list of tools but otherwise LGTM

[TCLamnidis]

Citation is there already given it is already used for damage rescaling!

eager/README.md

Line 249 in 631f18e

* **mapDamage2** Jónsson, H., et al 2013. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics , 29(13), 1682–1684. [https://doi.org/10.1093/bioinformatics/btt193](https://doi.org/10.1093/bioinformatics/btt193)

[TCLamnidis]

Added mapDamage to Default Pipeline Steps in README. Standardised tool name to mapDamage across all docs (as the name is in the GH repository of the tool)

[TCLamnidis]

Will wait for mapdamage module to be added to multiqc, then should be ok to merge

[jfy133]

Should add a big fat warning top of the readme sayi g maximum NDC aversion of 22.10.6

[TCLamnidis]

Regarding the Bowtie read groups, the suggested edits would also need to be propagated to the bwa job.
Specifically:

• Changing the RG-ID to the sample name from the library name, and
• adding a separate field to the RG with the library ID

[jfy133]

mapdamage stuff looks good, lets wait for feedback on the RG

[TCLamnidis]

TODO:
MultiQC does not pick up the mapdamage outputs locally, even though they are correctly published within the work directory and the module is activated. Have to check what is wrong.

[TCLamnidis]

I think that's everything!

[jfy133]

LGTM assuming old linting working and tests pass

[TCLamnidis]

@ltcrod Please have a look at the RG information for the mappers. Let me know if anything would be better implemented differently.

[TCLamnidis]

Linting works with nf-core v1.14. only failures are about template matching.