Third umi read

[adamrtalbot]

Support for UMI sequences contained in third read, e.g. Nonacus or IDT.

• Adds new column to samplesheet fastq_umi for UMI

Additions:

• Writes software versions in versions.yml

Fixes:

• Catches BWA indexes that include .64

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/fastquorum 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).

[nh13]

@adamrtalbot thanks for the submission. It's on my list to review but that may take a little while.

[nh13]

@adamrtalbot : can you get the tests passing (let me know if you want me to help)?

[nh13]

@adamrtalbot would you have a link to the protocol for both Nonacus or IDT, along with a test dataset (or datasets) we could add here: https://github.com/nf-core/test-datasets/tree/fastquorum

[adamrtalbot]

Hi @nh13, I don't have immediate access to either of those things but I can ask my former colleagues. IDT have a diagram here but limited instructions: https://www.idtdna.com/pages/support/faqs/how-do-i-sequence-the-umi-in-the-xgen-udi-umi-adapters

An existing PR for a UMI FASTQ file is here: nf-core/test-datasets#703, I will re-point this one to the fastquorum branch.

I'll take a look at updating this PR soon, sorry it fell by the wayside.

[adamrtalbot]

PR for test data open here: nf-core/test-datasets#1201

[adamrtalbot]

Closed in favour of #37