Refactor + updates to gens and germlinecnvcaller

[ramprasadn]

This PR

• Updates germlinecnvcaller subworkflow to use mappability and segmental duplications track
• Updates germlinecnvcaller and gens subworkflows to use custom names for panel of normals.
• Addresses Add igenomes support #23

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/createpanelrefs branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
• 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).

[maxulysse]

why user?

[ramprasadn]

This worklfow can also generate these files if not provided by the user so just to differentiate user given and pipeline generated dict and fai, I use user here :)

[maxulysse]

why?
I'd assume that either user generated or pipeline generated fai/dict from the same fasta file should correspond, no?

[ramprasadn]

The files should correspond, yes. This is more for code readability, because I do this later

createpanelrefs/subworkflows/local/germlinecnvcaller_cohort.nf

Lines 36 to 44 in 7a8d930

	ch_user_dict
	.mix(PICARD_CREATESEQUENCEDICTIONARY.out.reference_dict)
	.collect()
	.set { ch_dict }
	ch_user_fai
	.mix(SAMTOOLS_FAIDX.out.fai)
	.collect()
	.set { ch_fai }

[maxulysse]

I see.

OK for now, but let's move this bit outside of this subworkflow and create a general prepare genome subworkflow later on