Pipes

[muffato]

Closes #76 and #78

First steps towards 1.3.0. In this pull-request, I implemented these:

• Combined steps to improve the efficiency of the pipeline, especially on large genomes
• "crumble" is now run on every data type, not just PacBio

Before release, we'll need to make crumble optional and give users a choice of BAM/CRAM (#64). That'll be in another pull-request.

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
• [ ] 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).

[muffato]

Regarding the title of https://github.com/sanger-tol/readmapping/pull/91/commits/3d71db723a6100ee50b9e137b6e4901a01e1187f : that was the latest nf-core version at the time. There's now an even more recent version. But what actually mattered was the introduction of meta2 attached to the reference genome, which we can now use in conf/modules.config