new module: cnvkit/referencepooled

Is there an existing module for this?

• I have searched for the existing module

Is there an open PR for this?

• I have searched for existing PRs

Is there an open issue for this?

• I have searched for existing issues

Further Information

As mentioned in #12656, currently the cnvkit/reference module only seems to support generating a flat reference as you cannot provide coverage files to generate a pooled normal reference. Providing per-sample coverage files is mutually exclusive with the --targets/--antitargets flags (CNVkit's reference subcommand has two distinct modes and refuses to combine them), so a new module for generating a pooled reference is required

Are you going to work on this?

• If I'm planning to work on this module, I added myself to the Assignees to facilitate tracking who is working on the module

Software requirements (conda)

---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
  - conda-forge
  - bioconda
dependencies:
  - bioconda::cnvkit=0.9.14

Read the existing cnvkit/reference module and the context in issue #12656 first, then review CNVkit 0.9.14's pooled-reference mode and the repository's module conventions. Done means adding cnvkit/referencepooled so per-sample coverage files can generate a pooled normal reference without combining them with --targets or --antitargets.