Migrate narfmap/hashtable to topic channels

[xHaMMaDy]

Description

• replace the legacy versions.yml output with a versions_narfmap tuple broadcast to topic: versions
• use dragen-os --version 2>&1 to report the NARFMAP version
• update the module metadata, nf-tests, and generated snapshots for the structured version output

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PR checklist

Closes #12319

• This comment contains a description of changes (with reason).
• Tests cover the changed version output.
• Remove all TODO statements.
• Broadcast software version numbers to topic: versions.
• 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.

Tests

• nf-core modules lint narfmap/hashtable (59 passed)
• Docker nf-test (2 passed)
• Singularity nf-test (2 passed)
• Micromamba nf-test using the Conda environment (2 passed)

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[SPPearce]

What is this for?

[LouisLeNezet]

Hi @xHaMMaDy,
Would you have some time to finish this PR ?

[LouisLeNezet]

This line should be as a separate assertion outside the snapshot.

[LouisLeNezet]

I meant

            assertAll (
                { assert process.success },
                { assert file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") } },
                { assert snapshot(
                    process.out.bam.collect { meta, bamFile -> [meta, file(bamFile).name, bam(bamFile).getReadsMD5()] },
                    process.out.findAll { key, val -> key.startsWith("versions") },
                ).match() }
            )

[LouisLeNezet]

You just need now to update the meta and snapshot

[LouisLeNezet]

I meant

            assertAll (
                { assert process.success },
                { assert file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") } },
                { assert snapshot(
                    process.out.bam.collect { meta, bamFile -> [meta, file(bamFile).name, bam(bamFile).getReadsMD5()] },
                    process.out.findAll { key, val -> key.startsWith("versions") },
                ).match() }
            )

[xHaMMaDy]

Pushed an update for the align test snapshots.

meta.yml already mirrors the simplified Samtools eval from main.nf.

I also tested the exact getReadsMD5() form locally for the segfault regression fixture, but it fails inside HTSJDK because the emitted BAM contains an invalid sequence name:

htsjdk.samtools.SAMException: Sequence name ... doesn't match regex

So for this specific malformed-BAM regression test, I moved the decompHash log check outside the snapshot, kept the BAM existence/non-empty checks outside the snapshot, and snapshot only the BAM meta/name plus versions. The normal BAM tests still use getReadsMD5().

Local checks:

• narfmap/align/tests/segfault.nf.test passes with Docker and Nextflow 25.10.2
• narfmap/align/tests/main.nf.test --update-snapshot passed and updated the normal BAM snapshots
• one full targeted local run hit a transient raw.githubusercontent.com staging timeout, and the isolated retry of that same shard passed

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