fix(modules): replace invalid touch .gz stubs with valid gzip

[HReed1]

Description

Fixes #5409. Replaces touch filename.gz with echo '' | gzip > filename.gz in stub blocks for 8 modules. Empty files created by touch are not valid gzip and cause EOFException in nf-test snapshot assertions.

After this PR, git grep -cP "touch .*\.gz(\\s+.*)*$" -- 'modules/' returns zero matches across the entire repository.

Modules Fixed

• bowtie2/align — unmapped .fastq.gz stubs (supplementary to PR Updated a bunch of modules that failed nf-test because of the generation of compressed files using touch #7978)
• gatk4/haplotypecaller
• metamdbg/asm
• pharokka/installdatabases
• popscle/freemuxlet
• rastair/methylkit
• staramr/search
• vt/decomposeblocksub

Fix Pattern

- touch ${prefix}.output.vcf.gz
+ echo '' | gzip > ${prefix}.output.vcf.gz

PR Checklist

• This comment contains all information about changes made
• All touch filename.gz replaced with echo '' | gzip > filename.gz
• No other changes to module logic, meta.yml, or tests
• Snapshot updates may be needed — happy to run nf-core modules test --update if requested

[HReed1]

@nf-core-bot fix linting

[HReed1]

CI Lint Failures — Pre-existing, Unrelated to This PR

The 4 remaining lint failures are pre-existing issues on master, unrelated to the touch → echo "" | gzip > stub fix in this PR:

Module	Failing Lint Test	Related to this PR?
popscle/freemuxlet	main_nf_version_topic	❌ No — module does not emit software versions as topic
rastair/methylkit	main_nf_version_topic, bioconda_latest, container_links	❌ No — outdated conda/container + missing version topic
staramr/search	main_nf_version_topic, bioconda_latest	❌ No — outdated conda + missing version topic
vt/decomposeblocksub	main_nf_version_topic	❌ No — missing version topic emit

These modules already fail nf-core modules lint on the current master branch. The only change in this PR is replacing touch filename.gz with echo "" | gzip > filename.gz in stub blocks — no other module logic, version emits, or container definitions were modified.

The 4 modules that only had the stub issue (bowtie2/align, gatk4/haplotypecaller, metamdbg/asm, pharokka/installdatabases) all pass lint cleanly ✅

[famosab]

Suggested change

	create_unmapped = save_unaligned ? "echo '' | gzip > ${prefix}.unmapped_1.fastq.gz && echo '' | gzip > ${prefix}.unmapped_2.fastq.gz" : ""
	create_unmapped = save_unaligned ? "echo | gzip > ${prefix}.unmapped_1.fastq.gz && echo | gzip > ${prefix}.unmapped_2.fastq.gz" : ""

FYI: just echo | gzip is enough :) but as is is fine

[HReed1]

Thanks for pointing that out! I had templated echo "" uniformly in my local AST mutation script to be overly cautious, but I agree your suggestion is much cleaner. I'm going to go ahead and make those updates. Brb!

[HReed1]

Updated! All 8 modules now use echo | gzip > with the quotes dropped, as suggested. Pushed as a new commit.

Separately, while building the AST mutation script for this fix, my analysis also flagged ~44 additional modules that are completely missing stub: blocks entirely. I'm tracking that work under 4570 to keep this PR scoped strictly to the touch .gz → echo | gzip fix.

[famosab]

I think you either need to swap the failed modules to topics as well here or @mashehu overwrites and merges :D

[mashehu]

i can force merge, once @famosab suggestions have been accepted

[famosab]

I think we are good to go @mashehu