Add --save_domtblout option - #71
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erikrikarddaniel merged 2 commits intoAug 24, 2026
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Picks up nf-core/modules#12772, which adds a save_domtblout take parameter and a domain_summary emit, so a calling pipeline can turn on hmmsearch's --domtblout output. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01PDswY3eJxbJ9xnWSCQFVRG
hmmsearch's per-sequence hit table carries no alignment coordinates, so
there was no way to work out how much of a profile a hit covers, or to
find a gene split over several adjacent ORFs where no single ORF covers
enough of the profile to be classified on its own. Those coordinates only
exist in the per-domain table, which the pipeline never wrote and which
could not be turned on from a config either.
--save_domtblout passes save_domtblout through to
FASTA_HMMSEARCH_RANK_FASTAS, which hands it to HMMER_HMMSEARCH as its
write_domain flag. No publishing change is needed: the module already
declares path('*.domtbl.gz') and the default publishDir puts it in
results/hmmer/.
The test_phylosearch_input profile now sets the option so the existing
pipeline test covers it. The table's footer embeds the work directory
path and a run timestamp, so its content is never reproducible and it is
added to tests/.nftignore; the snapshot records the filenames only.
Also corrects docs/output.md, which listed hmmsearch's human-readable
output as *.tbl.gz, a duplicate of the line above it, rather than
*.txt.gz.
Closes nf-core#69
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01PDswY3eJxbJ9xnWSCQFVRG
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erikrikarddaniel
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August 24, 2026 09:48
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).Description
Closes #69.
hmmsearch's per-sequence hit table carries no alignment coordinates, so there was no way to work out how much of a profile a hit covers, or to find a gene split over several adjacent ORFs where no single ORF covers enough of the profile to be classified on its own. Those coordinates only exist in the per-domain table, which the pipeline never wrote and which could not be turned on from a config either:ext.args = "--domtblout …"produces a file the module never gzips and no declared output pattern matches, and overridingpublishDirforHMMER_HMMSEARCHfrom a-cconfig disabled publishing for that process entirely.The blocker was upstream:
fasta_hmmsearch_rank_fastashardcodedwrite_domaintofalse. nf-core/modules#12772 added asave_domtblouttake:parameter and adomain_summaryemit, and is now merged, so this PR updates the vendored subworkflow and wires the option through.Changes
fasta_hmmsearch_rank_fastasto56521ad, the merge commit of Support save_domtblout in fasta_hmmsearch_rank_fastas modules#12772.--save_domtbloutparameter (defaultfalse), passed as an explicit value frommain.nfintoPHYLOPLACEand on toFASTA_HMMSEARCH_RANK_FASTAS, per the pipeline's existing convention of not readingparams.*belowmain.nf.HMMER_HMMSEARCHalready declarespath('*.domtbl.gz'), emit: domain_summaryand gzips it, so the defaultpublishDirinconf/modules.configlands it inresults/hmmer/.### Saving the per-domain hit tablesection indocs/usage.md, and the*.domtbl.gzoutput listed indocs/output.md. While there, correcteddocs/output.md, which listedhmmsearch's human-readable output as*.tbl.gz, a duplicate of the line above it, rather than*.txt.gz.Testing
conf/test_phylosearch_input.confignow setssave_domtblout = true, so the existing pipeline test covers the new path end to end rather than adding another full pipeline run to CI. The trade-off is that the phylosearch path no longer has a test with the option off.The table's footer embeds the work directory path and a run timestamp, so its content is never reproducible;
hmmer/*.domtbl.gzis therefore added totests/.nftignoreand the snapshot records the filenames only. Verified stable by re-running the suite without--update-snapshot, not just recorded once.Full
nf-test test --profile=+dockersuite passes (6/6).nf-core pipelines lintreports 0 failures.nextflow lint .is clean on 26.04.6; on the declared minimum 25.10.4 the one remaining error is pre-existing in the vendoredutils_nextflow_pipelinesubworkflow and untouched here.Not included
Issue #69 also mentions
SEQTK_SUBSEQoutput filenames missing a separator (domain_16s.fnaarc.fa.gz). That comes from the vendoredseqtk/subseqmodule building its output name as${sequences}${prefix}.${ext}.gz, so it cannot be fixed from this pipeline withext.prefix. It needs a fix in nf-core/modules and will be picked up in the next general module update here.