2.1 update clean up notes

[jfy133]

Authors

• [x] Update author list in license/docker file to all expected final publication coauthors
• [x] Syncronise README for authors/contributors
• [x] Syncronise Manifest in nextflow .configs
• [x] Update authors in in main.nf header

MultiQC

• [x] MultiQC config missing software versions report placement (and check how this works)
• [ ] Add more File Cleanup Strings to MultiQC yaml to have samples merged if possible

Main.nf

• [x] Example command is missing required fasta in help message in main.nf
• [x] Missing Kraken and endorS.py commands in get software versions process

Tests

• [x] Try to get GATK 3.5 GithubActions to work

get_software_versions

• [x] Missing Kraken regex
• [x] Missing endorS.py regex

PR Template

• [x] Add note saying added new tool - added to get_softeware_versions process and python script.

[apeltzer]

MultiQC is up to you now ;-)

Main.nf example command update too - once we have that, we can release I guess.

[apeltzer]

Readme has full list now. Contributors are sorted alphabetically now too.

The manifest file is too long for tower.nf if we keep it complete - I replaced it there with "the nf-core/eager community", same in the dockerfile. The main.nf refers to the readme on the webpage now too - I think this is fine for everyone 👍

[jfy133]

Will do remaining points, and will split authors Vs contributors - as discussed on slack.

Will also try get GATK 3.5 GitHub actions test to work but not important.

[jfy133]

Going to leave " Add more File Cleanup Strings to MultiQC yaml to have samples merged if possible" until 2.2

Will do a big overhaul of MultiQC stuff when 1.9 comes out as that will bring a lot of waited-upon functionality. TSV input will also make this much easier to standardise what we clip off.