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

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

[TCLamnidis]

still need:

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

[TCLamnidis]

Citation is there already given it is already used for damage rescaling! https://github.com/nf-core/eager/blob/631f18efa4147d0b787245ed8dda041d00ebf6fd/README.md?plain=1#L249

[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

[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!

[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.