Added Trimmomatic, support contig for bining, set concoct default parameters

[Pranjal-Bioinfo]

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 - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/mag branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• 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).

[sateeshperi]

need to make the use of scaffolds/contigs for binning a param rather than a replacement

[GallVp]

need to make the use of scaffolds/contigs for binning a param rather than a replacement

I have added a new parameter spades_use_contigs_not_scaffolds, rebased the branch on top of the current dev and restored logos to pass the lint checks. I can see that CHANGELOG.md has not been updated and there isn't any issue linked to this PR. Anyone of us taking care of that?

[sateeshperi]

closes #744

[sateeshperi]

LGTM now....lets get a review from #mag ppl

[jfy133]

• Please add running trimmomatic to one of the test configs so we know it can execute at least once

And generally missing docs!

• Listing in the README
• Missing output.md

Otherwise code looks good! Just some consistency things

[jfy133]

@Pranjal-Bioinfo I'm assuming you're still busy, so I'll take this over for the last bit, and include it in the next release

[jfy133]

Made a few changes but otherwise LGTM!

@sateeshperi want to be included in the CHANGELOG as it looks like you somewhat supervised?

[GallVp]

Hi @sateeshperi

This is ready now. Kindly have a look when you have some time.

[prototaxites]

Hi all, looks good to me! A couple of very minor comments + 1 query about template changes

[sateeshperi]

Need to update docs/usage.md to indicate how to use configs/scaffolds and chunk size and overlap params.

[jfy133]

What do you mean exactly @sateeshperi ?

Generally I don't describe parameters much in usage.md, there are so many parameters in mag it would basically duplicate the parameters tab :smile_sweat:, unless you had a specific idea?

Eventually I would like ot write proper tutorials where I think such information would be more useful.

[sateeshperi]

makes sense

[jfy133]

Woohoo! Thank you very much @Pranjal-Bioinfo @GallVp @sateeshperi @prototaxites ! Team effor ton this one :D