Fix file extension for module PBMARKDUP

[sainsachiko]

Fix file extension to:

• Get right extension for .gz file
• As the tool can take multiple input types and write to 1 single output, modify code to suit with tool's convention:

PR checklist

Closes #XXX

• This comment contains a description of changes (with reason).
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[Copilot]

Pull request overview

This PR refines the PBMARKDUP module’s handling of input file extensions so that outputs follow the tool’s convention when given multiple input types, including compressed FASTA/FASTQ, and updates the associated tests and snapshots accordingly.

Changes:

• Update PBMARKDUP process logic to derive the output suffix from the actual input filenames, including correctly preserving compound extensions such as .fastq.gz and .fasta.gz.
• Adjust nf-test specifications for pbmarkdup to cover multiple input patterns (single FASTA, multiple BAMs, and mixed FASTA/FASTQ inputs with dupfile+log options).
• Regenerate the nf-test snapshot file with new test names, expected outputs (including dupfile and log channels), and newer nf-test and Nextflow version metadata.

Reviewed changes

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

File	Description
modules/nf-core/pbmarkdup/main.nf	Changes suffix calculation to search the input list for FASTA/FASTQ filenames (including .gz), derive the appropriate extension fragment, and fall back to the first input’s extension, ensuring the module’s single-output filename matches the primary input type.
modules/nf-core/pbmarkdup/tests/main.nf.test	Renames and restructures tests to exercise multiple input types and the dupfile/log behaviour, including a new mixed FASTA/FASTQ test, while keeping stub and single-input FASTA coverage.
modules/nf-core/pbmarkdup/tests/main.nf.test.snap	Updates snapshot keys and expected outputs to align with the new test names and behaviours (including null.dup.bam dupfile outputs and test.pbmarkdup.log logs), and records the newer nf-test/Nextflow versions and timestamps.

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[Copilot]

Here pbmarkdup_args uses ${prefix} inside a Groovy double-quoted string, but prefix is not defined in this nf-test parameter scope, so it interpolates to the literal string null (reflected by the null.dup.bam filenames in the snapshot). To avoid this surprising behaviour and better reflect the intention of tying the duplicate file name to the module’s output prefix, consider either using an explicit fixed dup file name here or passing the desired prefix via task.ext.prefix instead of relying on ${prefix} in the params string.

[Copilot]

The new suffix resolution logic adds explicit handling for compressed FASTA/FASTQ inputs (e.g. .fasta.gz, .fastq.gz), but the updated pbmarkdup tests only cover uncompressed fasta/fastq and BAM inputs, so the .gz branch isn’t exercised. Given this module already has nf-test coverage, it would be worthwhile to add at least one test using a .fasta.gz or .fastq.gz input to verify that the output file name preserves the full compressed extension as intended.

[sainsachiko]

Updated with a test with fastq.gz. However, it seem output fastq.gz from pbmarkdup is actually not a gz file, just a normal fastq. I have included gzip step for .gz input, otherwise, md5sum for this mal-formed fastq.gz is unstable @SPPearce

[SPPearce]

Add a closure to be able to use the prefix I think.
If it doesn't work, then just hardcode it, it'd normally be set with a closure.

Suggested change

	pbmarkdup_args = "--clobber --dup-file ${prefix}.dup.bam --log-level INFO"
	pbmarkdup_args = { "--clobber --dup-file ${meta.id}.dup.bam --log-level INFO" }

[sainsachiko]

Somehow I can not used both of it, possibly because args is now stated in main.nf.test then included in nextflow.config (it is compile before, when meta is still a null object ?!).
Thus I have just simply put a string as a name for dup file. Users can use meta.id or ext.prefix if they specify it right in config block.

[SPPearce]

The AI comments are sensible too.

[SPPearce]

This is an nf-test error, it happens when you touch a .gz file. It needs to be echo | gzip > test.dup.fastq.gz instead to prevent this from happening.

[sainsachiko]

Oh I see, thank you for pointing that out @SPPearce . It seems to happen inside pbmarkdup when the tool write .fq.gz file. With the new gzip code introduced in 577e272, this should be fine as it gzip to a new file and export that new file.