Audit: Module directory names that don't match the tool invoked in script block

Summary

An automated scan of all 1767 nf-core modules found 39 modules where the directory name (modules/nf-core/<tool>/<subtool>/) does not match the actual command invoked in the script: block of main.nf. Per nf-core convention, modules should follow tool/subtool naming that matches the CLI tool being called.

This issue was prompted by the discussion in #10959 (comment) about mcstaging/* modules being grouped by purpose rather than by tool name.

Each case below needs human review to determine the appropriate action (rename, restructure, or document as acceptable exception).

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Mismatches by Category

🔬 Imaging / mcmicro modules (grouped by purpose instead of tool)

These modules are grouped under umbrella directories by function rather than by tool name:

Reviewed?	Module path	Dir tool name	Actual command	Notes
deprecated by @kbestak	mcstaging/imc2mc	mcstaging	python /imc2mc/scripts/imc2mc.py	Tool is imc2mc, grouped under mcstaging
	mcstaging/macsima2mc	mcstaging	python /staging/macsima2mc/macsima2mc.py	Tool is macsima2mc
	mcstaging/phenoimager2mc	mcstaging	python /phenoimager2mc/scripts/phenoimager2mc.py	Tool is phenoimager2mc
	vizgenpostprocessing/compiletilesegmentation	vizgenpostprocessing	vpt	Tool is vpt (Vizgen Postprocessing Tool)
	vizgenpostprocessing/preparesegmentation	vizgenpostprocessing	vpt	Tool is vpt
	vizgenpostprocessing/runsegmentationontile	vizgenpostprocessing	vpt	Tool is vpt
	coreograph	coreograph	python /app/UNetCoreograph.py	Script is UNetCoreograph.py
	basicpy	basicpy	/opt/main.py	Container-embedded script, no basicpy CLI binary (borderline)

🧬 Tool suite vs. individual tool binary

The directory uses a suite/package name but the script calls a differently-named binary from that suite:

Reviewed?	Module path	Dir tool name	Actual command	Notes
@famosab : leave as is because fibertools is more descriptive and the actual tool name, acceptable exception	fibertoolsrs/addnucleosomes	fibertoolsrs	ft	fibertools-rs installs as ft
same	fibertoolsrs/extract	fibertoolsrs	ft	Same
same	fibertoolsrs/predictm6a	fibertoolsrs	ft	Same
@famosab : I would say if we want to be really strict these modules should be called tama/.. but as that would need deprecation and gstama is not completely wrong I would leave them as is, acceptable exception	gstama/collapse	gstama	tama_collapse.py	Conda pkg is gs-tama, tool is tama
same	gstama/merge	gstama	tama_merge.py	Same
same	gstama/polyacleanup	gstama	tama_flnc_polya_cleanup.py	Same
@famosab: leave as is, the tool never uses the suite name in the subscripts but the nf-core module naming is compliant to our guidelines, acceptable exception	cmseq/polymut	cmseq	polymut.py	cmseq is the suite, polymut is the specific tool
	vrhyme/extractunbinned	vrhyme	extract_unbinned_sequences.py	Helper script in vRhyme, not vRhyme itself
	vrhyme/linkbins	vrhyme	link_bin_sequences.py	Same
	fcs/fcsadaptor	fcs	av_screen_x	Internal NCBI FCS-adaptor binary name

📦 Conda package name vs. CLI binary name

The directory uses the Conda package name, but the installed binary has a different name:

Reviewed?	Module path	Dir tool name	Actual command	Notes
	dragmap/align	dragmap	dragen-os	DragMap package installs dragen-os binary
	dragmap/hashtable	dragmap	dragen-os	Same
	pbccs	pbccs	ccs	PacBio Conda pkg pbccs, binary is ccs
	pbjasmine	pbjasmine	jasmine	Conda pkg pbjasmine, binary is jasmine
	biohansel	biohansel	hansel	Conda pkg bio_hansel, binary is hansel
	kofamscan	kofamscan	exec_annotation	kofamscan installs exec_annotation as its CLI
	variantbam	variantbam	variant	VariantBam binary is just variant

🔧 Wrapper/parallel tools with different names

Reviewed?	Module path	Dir tool name	Actual command	Notes
@famosab: can be left as is, we like parallelization but its not needed to be part of the module name, acceptable exception	ltrfinder	ltrfinder	LTR_FINDER_parallel	Parallel wrapper, not ltr_finder itself
@famosab: I think the meta.yml is wrong, gt never appears in the script block, I would say correct the meta and we are good	ltrharvest	ltrharvest	LTR_HARVEST_parallel	Parallel wrapper (note: gt/ltrharvest correctly calls gt ltrharvest)

🏷️ Functional/descriptive names instead of tool names

Reviewed?	Module path	Dir tool name	Actual command	Notes
	unzip	unzip	7za	Calls p7zip, not unzip
	unzipfiles	unzipfiles	7za	Same
	zip	zip	7z	Calls p7zip, not zip
	shasum	shasum	sha256sum	macOS shasum vs GNU sha256sum
	amps	amps	postprocessing.AMPS.r	Actually calls HOPS package script
	multiqcsav	multiqcsav	multiqc	Calls multiqc with SAV plugin, not a standalone tool

🔀 Subcommand under wrong parent

Reviewed?	Module path	Dir tool name	Actual command	Notes
@famosab: this command is now callable as bcftools roh-viz, the module script should be updated to reflect this	bcftools/rohviz	bcftools	roh-viz	Standalone tool, not a bcftools subcommand
@famosab: leave as is, the tool never uses the suite name in the subscripts but the nf-core module naming is compliant to our guidelines, acceptable exception	genotyphi/parse	genotyphi	parse_typhi_mykrobe.py	Script name doesn't match directory
@famosab: the tool author is inconsistent in their naming, acceptable exception	gens/preparecovandbaf	gens	generate_cov_and_baf	CLI entry point doesn't match directory
	macsyfinder/download	macsyfinder	msf_data install	Separate database management tool
	checkm2/databasedownload	checkm2	aria2c	Just a download; checkm2 never called

🌐 Platform/runtime tools

Reviewed?	Module path	Dir tool name	Actual command	Notes
@famosab: acceptable exception	deeptmhmm	deeptmhmm	biolib run DTU/DeepTMHMM	Runs via BioLib platform CLI

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Methodology

• Automated scan of all 1767 module main.nf files
• Compared directory tool name against the primary command in the script: block
• Excluded shell builtins (cat, echo, mkdir, etc.) and version-reporting blocks
• Minor variations (case, hyphens, version suffixes like gatk4→gatk) were not flagged
• Each finding needs human review — some may be acceptable exceptions

Suggested Actions

For each module, the community should decide:

1. Rename the module directory to match the actual tool (preferred for most cases)
2. Accept as exception with documentation (e.g., functional modules like unzip/zip)
3. Move to pipeline-local if the module is too pipeline-specific for the shared repository

Context

• PR discussion: #10959
• Convention: modules should be tool/subtool matching the CLI call
• Related: imaging community modules grouped by purpose rather than tool name

Start with the listed module paths and inspect each module's main.nf script block, using the naming convention and PR #10959 discussion as context. For every mismatch, determine whether to rename or restructure the module, document it as an acceptable exception, or move it pipeline-local. Done means all 39 cases have a recorded community decision.