Template/update

[anoronh4]

Pipeline template update

Some well overdue pipeline template updates. Because there hasn't been a sync in so long i had to follow the sync retrospectively guide, but now that we are in sync we should in the future be able to follow the manual sync guide, provided we don't wait too long between updates.

Some highlights in the update:

1. pipeline initialization has been structured differently as a subworkflow rather than groovy library methods. prints version info, summarizes and dumps pipeline parameters, validates parameters, and now reads in and validates the input samplesheet.
2. The fastq samplesheet is now validated using nf-schema and the definition file assets/schema_input.json. The maf input file is also now validated using nf-schema using a separate definition file assets/schema_maf_input.json.
3. software dump prints to a different file in the same location and pipeline template now has different logic for generating it.
4. pipeline completion workflow added, which sends emails upon completion or failure.

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 mskcc/forte 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 --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).

[anoronh4]

it might make sense to create a new branch off of develop called dev and use that instead. the template wants dev and our code keeps getting incongruous because i for some reason chose develop.