Add step markduplicates & allow BAM input for all steps

[FriederikeHanssen]

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 - add to the software_versions process and a regex to scrape_software_versions.py
  • 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/sarek 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).
• 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 not adding DEEPTOOLS_BAMCOVERAGE to nf-core/cram_qc.nf and control in conf/modules.config which qc tools we use?

[FriederikeHanssen]

why not adding DEEPTOOLS_BAMCOVERAGE to nf-core/cram_qc.nf and control in conf/modules.config which qc tools we use?

hm yeah that would work, or I thought also that we could rewrite bam_qc to run the QC tools on cram both and just control SAMTOOLS_BAMTOCRAM whether it is cram input or not.

[marissaDubbelaar]

LGTM, two minor suggestions

[ggabernet]

Hey Looks good to me! I've just thought that if you changed that the step prepare_recalibration works maybe that should also be added to the docs, but maybe you plan to add all docs in a separate PR, that's also fine :)

[FriederikeHanssen]

Hey Looks good to me! I've just thought that if you changed that the step prepare_recalibration works maybe that should also be added to the docs, but maybe you plan to add all docs in a separate PR, that's also fine :)

Yes I am planning to do everything in the docs at once, but it is probably a good idea to at least put a note into the docs so i won't loose track.

Thanks a lot for reviewing 🙏