Add rtgtools/cnveval module for CNV evaluation

[SevaNur]

PR checklist

Closes #266

• 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 module conventions in the
• If necessary, include test data in your PR.
• Remove all TODO statements.
• Broadcast software version numbers to topic: versions - See version_topics
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda

Description

Add new module rtgtools/cnveval for evaluating called CNV regions against a baseline CNV set.

rtg cnveval intersects evaluation regions (BED) with truth and calls VCFs to obtain TP/FP/FN metrics for copy number variants. Input VCFrecords must contain INFO/END and INFO/SVTYPE with values DUP or DEL.

Outputs:

• baseline.bed.gz — truth CNV regions with TP/FN status
• calls.bed.gz — called CNV regions with TP/FP status
• weighted_roc.tsv.gz — ROC data for rocplot
• summary.txt — summary statistics

Uses existing test data from nf-core/test-datasets (simulated_sv.vcf.gz, simulated_sv2.vcf.gz).

[georgiakes]

Nice job! Looks good to me :)

[SPPearce]

Suggested change

	tuple val(meta), path("*.baseline.bed.gz") , emit: baseline_bed
	tuple val(meta), path("*.calls.bed.gz") , emit: calls_bed
	tuple val(meta), path("*.weighted_roc.tsv.gz") , emit: weighted_roc
	tuple val(meta), path("*.summary.txt") , emit: summary
	tuple val(meta), path("*.baseline.bed.gz") , emit: baseline_bed
	tuple val(meta), path("*.calls.bed.gz") , emit: calls_bed
	tuple val(meta), path("*.weighted_roc.tsv.gz"), emit: weighted_roc
	tuple val(meta), path("*.summary.txt") , emit: summary

[SPPearce]

I don't know what the mv done progress .. part is doing here.
But you should be able to move without the two cd's

[SPPearce]

Suggested change