Support CRAM in the hifitrimmer module

[muffato]

To complete the support matrix of the module (and our readmapping pipeline). Support for (unaligned) CRAM

Requires nf-core/test-datasets#1950

PR checklist

Closes #XXX

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[Copilot]

Pull request overview

This PR extends the nf-core/hifitrimmer/filterbam module to support (unaligned) CRAM inputs, completing the module’s supported input formats for downstream readmapping usage.

Changes:

• Add CRAM handling to HIFITRIMMER_FILTERBAM by converting CRAM to BAM on-the-fly via samtools view.
• Add an nf-test case for CRAM input and record the expected snapshot output.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 2 comments.

File	Description
modules/nf-core/hifitrimmer/filterbam/main.nf	Adds CRAM-specific input conversion logic prior to running hifi_trimmer filter_bam.
modules/nf-core/hifitrimmer/filterbam/tests/main.nf.test	Adds a new test scenario for CRAM input.
modules/nf-core/hifitrimmer/filterbam/tests/main.nf.test.snap	Adds snapshot expectations for the new CRAM test.

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[prototaxites]

Looks good - looks like you need a new container to pin the latest version of samtools.

Otherwise, one small comment.

[prototaxites]

LGTM!

[muffato]

Thank you !