Add taxonomy summary table with per-ASV barrnap/decontam/filter annotations

[erikrikarddaniel]

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/ampliseq branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

Description

Closes the last piece of issue #1033: a per-classifier taxonomy summary table, joined with per-ASV
annotations from barrnap, decontam, and the optional post-processing filters.

summary_tables/ampliseq.taxonomy.<classifier>.<database>.tsv.gz (+ Parquet)

One file per classifier/database already carried in ch_tax_tsv (Kraken2 excluded -- its rank
vocabulary and output shape are too different to normalize). A slim, consistent-schema reformat of
that classifier's own native taxonomy table: asv_id, kingdom..species, confidence.
QIIME2's k__/p__-prefixed Taxon string and phylogenetic placement's unranked, semicolon-joined
string are both parsed into the same seven rank columns (best-effort for the latter). sequence is
dropped (recoverable via asv_id) and, for DADA2, the per-rank *_confidence columns are dropped
too (DADA2-specific detail, not comparable across classifiers) -- both remain available in full in
the native per-classifier files elsewhere in the output directory.

Joined onto every one of these files, whenever the corresponding step ran:

• barrnap_domain: the rRNA domain barrnap called with the lowest e-value for this ASV, blank if
  none was significant.
• decontam_contaminant / decontam_not_contaminant: decontam's own contaminant call.
• passed_ssu_filter, passed_length_filter_asv, passed_codon_filter,
  passed_length_filter_itsx: whether this ASV survived each individual optional filter.
• ampliseq_accept: whether this ASV survived the whole standard filtering chain (decontam through
  the ITSx-region length filter) end to end -- a convenience alongside the individual columns above,
  not instead of them, so the pipeline's own filtering choices can be recombined differently.

New module BUILD_ASV_ANNOTATIONS builds these by diffing each filter's ASV table immediately
before/after it runs (none of FILTER_SSU/FILTER_LEN/FILTER_CODONS emit a per-ASV pass/fail
column natively) -- purely additive plumbing, no change to the filter chain's own logic, order, or
gating. Tidyverse throughout (per-type long-format stacking + pivot_wider, split by value type
before stacking so Parquet gets real BOOLEAN/UTF8 columns rather than everything coerced through
one generically-typed column).

Also fixes a gap in the existing ampliseq.counts.tsv.gz/.parquet Parquet conversion (#1052):
DUCKDB_TABLE2PARQUET used to run immediately after SUMMARY_TABLE_COUNTS, before this PR's
taxonomy tables existed yet, so it silently never converted them. Moved to run once after every
summary table has been mixed into the shared channel.

Two real bugs found by review + testing, both fixed

• DADA2_ADDSPECIES always renames its own species call to Species_exact, only re-adding a native
  Species column when assignTaxonomy's own taxlevels included one -- databases that rely on
  addSpecies alone for species-level calls (e.g. RDP) would have silently had no species column at
  all. Fixed by coalescing species/species_exact (prefer the native assignTaxonomy call, fall
  back to addSpecies), verified against real RDP output.
• SUMMARY_TABLE_TAXONOMY needed .combine() against the annotations table -- without it, Nextflow
  silently dropped every ch_tax_tsv entry past the first, since a queue channel that only ever
  emits once isn't auto-broadcast against a multi-item channel the way a true value channel is.

Testing

• tests/default.nf.test, tests/multidb.nf.test, tests/pplace.nf.test, tests/sintax.nf.test,
  tests/vsearch_lca.nf.test all run for real (docker), with manual content spot-checks beyond the
  automated assertions -- e.g. confirming QIIME2's k__/p__ string and PPLACE's unranked string
  both parse into the right rank columns, and that the RDP species fix actually populates real data.
• The remaining profiles that run a non-Kraken2 classifier (fasta, glosed, multi, savont,
  savont_independent, single, pacbio_its, pplace_sheet, qiimecustom, reftaxcustom,
  failed, iontorrent) have their .nf.test.snap snapshots updated by hand rather than a full
  local run, based on tracing the exact classifier/database name each profile produces through the
  channel-building code (including the user database key used by every *_ref_tax_custom path).
  Flagging this explicitly in case CI surfaces a misprediction there.
• nf-core pipelines lint and prek run -a both clean, at the same baseline as dev (the
  pre-existing nextflow config -o json/SAVONT_ASV issue and a couple of unrelated files_unchanged
  checks aren't introduced by this PR).

[d4straub]

Didnt check the R script details, just in-person-code-browsing. Looks good so far I think. Just a few comments

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ecd0115

+| ✅ 319 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗ 114 tests had warnings |!

Details

❗ Test warnings:

• local_component_structure - dada2_addspecies.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - consolidate_dada2_taxonomy.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sidle_taxrecon.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - itsxrust_cutasv.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - summary_report.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - filter_ssu.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - format_taxonomy_sintax.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_ancom_asv.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_barplot.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sidle_dbrecon.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - format_taxonomy.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_diversity_betaord.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_tree.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - format_taxresults_vsearch_lca.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - format_taxresults.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - filter_sequences_abundances.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - savont_asv.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - dada2_merge.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_intree.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sidle_treerecon.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_diversity_adonis.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - format_fastainput.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - barrnap.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - decontam.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_export_absolute.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - itsx_cutasv.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sidle_dbfilt.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - phyloseq.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - dada2_denoising.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_export_relasv.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_ancombc2_asv.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_ancom_tax.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - metadata_all.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_seqfiltertable.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sidle_align.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_tablefiltertaxa.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - phyloseq_intax.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - treesummarizedexperiment.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_export_reltax.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - picrust.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - metadata_pairwise.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - combine_table.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - format_taxonomy_vsearch_lca.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_alphararefaction.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - merge_stats.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - assignsh.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - format_taxonomy_sidle.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - phyloseq_inasv.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - compare_performance.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - download_reference.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sidle_seqrecon.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - filter_codons.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_classify.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sidle_dbextract.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_featuretable_group.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sidle_in.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sidle_indbaligned.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sidle_filttax.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - format_taxresults_kraken2.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_filtersamples.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_ancombc_asv.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - barrnapsummary.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_extract.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - compare_sequences.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_diversity_core.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - format_taxonomy_qiime.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - cutadapt_summary.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - filter_samples.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - compare_profile.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_inasv.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sidle_trim.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_diversity_alpha.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sbdiexport.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - dada2_splitregions.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - dada2_rmchimera.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sidle_tablerecon.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_ancombc_tax.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_inseq.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - cutadapt_summary_merge.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sbdiexportreannotate.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - trunclen.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - dada2_stats.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - format_taxresults_sintax.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sidle_indb.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_train.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - format_pplacetax.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_ancombc2_tax.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_intax.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - dada2_taxonomy.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - dada2_filtntrim.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - dada2_err.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - dada2_quality.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - filter_stats.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - filter_len.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - savont_export.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_diversity_beta.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - filter_clusters.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - rename_raw_data_files.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_preptax.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - parse_input.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - dada2_preprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - sidle_wf.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - comparison_wf.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - qiime2_barplotavg.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - qiime2_ancom.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - kraken2_taxonomy_wf.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - qiime2_taxonomy.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - dada2_taxonomy_wf.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - vsearch_lca_taxonomy_wf.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - cutadapt_workflow.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - robject_workflow.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - qiime2_export.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - sintax_taxonomy_wf.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - qiime2_diversity.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

• files_exist - File is ignored: conf/igenomes.config
• nextflow_config - nextflow_config
• files_unchanged - File ignored due to lint config: .gitattributes
• files_unchanged - File ignored due to lint config: assets/nf-core-ampliseq_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-ampliseq_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-ampliseq_logo_dark.png
• files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
• schema_params - schema_params

✅ Tests passed:

• files_exist - File found: .gitattributes
• files_exist - File found: .gitignore
• files_exist - File found: .nf-core.yml
• files_exist - File found: .prettierignore
• files_exist - File found: .prettierrc.yml
• files_exist - File found: CHANGELOG.md
• files_exist - File found: CITATIONS.md
• files_exist - File found: CODE_OF_CONDUCT.md
• files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
• files_exist - File found: nextflow_schema.json
• files_exist - File found: nextflow.config
• files_exist - File found: README.md
• files_exist - File found: .github/.dockstore.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
• files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
• files_exist - File found: .github/workflows/branch.yml
• files_exist - File found: .github/workflows/nf-test.yml
• files_exist - File found: .github/actions/get-shards/action.yml
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• files_exist - File found: .github/workflows/pr-comment.yml
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• files_exist - File found: conf/modules.config
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• files_exist - File found: docs/CONTRIBUTING.md
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• files_exist - File found: docs/output.md
• files_exist - File found: docs/README.md
• files_exist - File found: docs/README.md
• files_exist - File found: docs/usage.md
• files_exist - File found: nf-test.config
• files_exist - File found: tests/default.nf.test
• files_exist - File found: main.nf
• files_exist - File found: assets/multiqc_config.yml
• files_exist - File found: conf/base.config
• files_exist - File found: conf/igenomes_ignored.config
• files_exist - File found: .github/workflows/awstest.yml
• files_exist - File found: .github/workflows/awsfulltest.yml
• files_exist - File found: modules.json
• files_exist - File found: ro-crate-metadata.json
• files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
• files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
• files_exist - File not found check: .github/workflows/push_dockerhub.yml
• files_exist - File not found check: .markdownlint.yml
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• files_exist - File not found check: conf/aws.config
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• files_exist - File not found check: lib/WorkflowMain.groovy
• files_exist - File not found check: lib/WorkflowAmpliseq.groovy
• files_exist - File not found check: parameters.settings.json
• files_exist - File not found check: pipeline_template.yml
• files_exist - File not found check: Singularity
• files_exist - File not found check: lib/nfcore_external_java_deps.jar
• files_exist - File not found check: .travis.yml
• nf_test_content - 'tests/glosed.nf.test' contains outdir parameter
• nf_test_content - 'tests/glosed.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/glosed.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/taxonomy_hash.nf.test' contains outdir parameter
• nf_test_content - 'tests/taxonomy_hash.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/multiregion.nf.test' contains outdir parameter
• nf_test_content - 'tests/multiregion.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/multiregion.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/failed.nf.test' contains outdir parameter
• nf_test_content - 'tests/failed.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/failed.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/multi.nf.test' contains outdir parameter
• nf_test_content - 'tests/multi.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/multi.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/reftaxcustom.nf.test' contains outdir parameter
• nf_test_content - 'tests/reftaxcustom.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/reftaxcustom.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/multidb_mixedranks.nf.test' contains outdir parameter
• nf_test_content - 'tests/multidb_mixedranks.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/multidb_mixedranks.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/doubleprimers.nf.test' contains outdir parameter
• nf_test_content - 'tests/doubleprimers.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/doubleprimers.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/single.nf.test' contains outdir parameter
• nf_test_content - 'tests/single.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/single.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/novaseq.nf.test' contains outdir parameter
• nf_test_content - 'tests/novaseq.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/novaseq.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/multidb_mostspecific.nf.test' contains outdir parameter
• nf_test_content - 'tests/multidb_mostspecific.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/multidb_mostspecific.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/vsearch_lca.nf.test' contains outdir parameter
• nf_test_content - 'tests/vsearch_lca.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/sintax.nf.test' contains outdir parameter
• nf_test_content - 'tests/sintax.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/sintax.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/fasta.nf.test' contains outdir parameter
• nf_test_content - 'tests/fasta.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/fasta.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/qiimecustom.nf.test' contains outdir parameter
• nf_test_content - 'tests/qiimecustom.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/qiimecustom.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/pplace_sheet.nf.test' contains outdir parameter
• nf_test_content - 'tests/pplace_sheet.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/pplace_sheet.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/savont_independent.nf.test' contains outdir parameter
• nf_test_content - 'tests/savont_independent.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/savont_independent.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/pacbio_its.nf.test' contains outdir parameter
• nf_test_content - 'tests/pacbio_its.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/pacbio_its.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/pplace.nf.test' contains outdir parameter
• nf_test_content - 'tests/pplace.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/pplace.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/multidb.nf.test' contains outdir parameter
• nf_test_content - 'tests/multidb.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/multidb.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/default.nf.test' contains outdir parameter
• nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/multidb_score.nf.test' contains outdir parameter
• nf_test_content - 'tests/multidb_score.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/multidb_score.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/savont.nf.test' contains outdir parameter
• nf_test_content - 'tests/savont.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/savont.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/iontorrent.nf.test' contains outdir parameter
• nf_test_content - 'tests/iontorrent.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/iontorrent.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
• nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
• nf_test_content - 'nf-test.config' sets a testsDir
• nf_test_content - 'nf-test.config' sets a workDir
• nf_test_content - 'nf-test.config' sets a configFile
• files_unchanged - .prettierrc.yml matches the template
• files_unchanged - CODE_OF_CONDUCT.md matches the template
• files_unchanged - LICENSE matches the template
• files_unchanged - .github/.dockstore.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
• files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
• files_unchanged - .github/workflows/branch.yml matches the template
• files_unchanged - .github/workflows/pr-comment.yml matches the template
• files_unchanged - .github/workflows/linting.yml matches the template
• files_unchanged - assets/email_template.html matches the template
• files_unchanged - assets/email_template.txt matches the template
• files_unchanged - assets/sendmail_template.txt matches the template
• files_unchanged - docs/README.md matches the template
• actions_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
• actions_nf_test - '.github/workflows/nf-test.yml' checks minimum NF version
• actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
• actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
• actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
• readme - README Nextflow minimum version badge matched config. Badge: 26.04.0, Config: 26.04.0
• readme - README nf-core template version badge found.
• readme - README Zenodo placeholder was replaced with DOI.
• pipeline_todos - No TODO strings found
• pipeline_if_empty_null - No ifEmpty(null) strings found
• plugin_includes - No wrong validation plugin imports have been found
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (0 files)
• schema_lint - Schema lint passed
• schema_lint - Schema title + description lint passed
• schema_lint - Input mimetype lint passed: 'text/tsv'
• system_exit - No System.exit calls found
• actions_schema_validation - Workflow validation passed: pr-comment.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: nf-test.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: awstest.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: template-version-comment.yml
• actions_schema_validation - Workflow validation passed: fix_linting.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: release-announcements.yml
• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json
• multiqc_config - assets/multiqc_config.yml found and not ignored.
• multiqc_config - assets/multiqc_config.yml contains report_section_order
• multiqc_config - assets/multiqc_config.yml contains export_plots
• multiqc_config - assets/multiqc_config.yml contains report_comment
• multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
• multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
• multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
• modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
• base_config - conf/base.config found and not ignored.
• modules_config - conf/modules.config found and not ignored.
• modules_config - DOWNLOAD_REFERENCE found in conf/modules.config and Nextflow scripts.
• modules_config - RENAME_RAW_DATA_FILES found in conf/modules.config and Nextflow scripts.
• modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
• modules_config - PORECHOP_ABI found in conf/modules.config and Nextflow scripts.
• modules_config - CHOPPER found in conf/modules.config and Nextflow scripts.
• modules_config - CUTADAPT_BASIC found in conf/modules.config and Nextflow scripts.
• modules_config - CUTADAPT_READTHROUGH found in conf/modules.config and Nextflow scripts.
• modules_config - CUTADAPT_DOUBLEPRIMER found in conf/modules.config and Nextflow scripts.
• modules_config - SAVONT_ASV found in conf/modules.config and Nextflow scripts.
• modules_config - SAVONT_EXPORT found in conf/modules.config and Nextflow scripts.
• modules_config - CUTADAPT_TAXONOMY found in conf/modules.config and Nextflow scripts.
• modules_config - CUTADAPT_SUMMARY_MERGE found in conf/modules.config and Nextflow scripts.
• modules_config - DADA2_QUALITY1 found in conf/modules.config and Nextflow scripts.
• modules_config - TRUNCLEN found in conf/modules.config and Nextflow scripts.
• modules_config - DADA2_FILTNTRIM found in conf/modules.config and Nextflow scripts.
• modules_config - DADA2_QUALITY2 found in conf/modules.config and Nextflow scripts.
• modules_config - DADA2_ERR found in conf/modules.config and Nextflow scripts.
• modules_config - DADA2_DENOISING found in conf/modules.config and Nextflow scripts.
• modules_config - DADA2_RMCHIMERA found in conf/modules.config and Nextflow scripts.
• modules_config - DADA2_STATS found in conf/modules.config and Nextflow scripts.
• modules_config - DADA2_MERGE found in conf/modules.config and Nextflow scripts.
• modules_config - SUMMARY_TABLE_COUNTS found in conf/modules.config and Nextflow scripts.
• modules_config - SUMMARY_TABLE_TAXONOMY found in conf/modules.config and Nextflow scripts.
• modules_config - DUCKDB_TABLE2PARQUET found in conf/modules.config and Nextflow scripts.
• modules_config - DADA2_SPLITREGIONS found in conf/modules.config and Nextflow scripts.
• modules_config - SIDLE_DBFILT found in conf/modules.config and Nextflow scripts.
• modules_config - SIDLE_DBEXTRACT found in conf/modules.config and Nextflow scripts.
• modules_config - SIDLE_TRIM found in conf/modules.config and Nextflow scripts.
• modules_config - SIDLE_ALIGN found in conf/modules.config and Nextflow scripts.
• modules_config - SIDLE_DBRECON found in conf/modules.config and Nextflow scripts.
• modules_config - SIDLE_TABLERECON found in conf/modules.config and Nextflow scripts.
• modules_config - SIDLE_TAXRECON found in conf/modules.config and Nextflow scripts.
• modules_config - SIDLE_FILTTAX found in conf/modules.config and Nextflow scripts.
• modules_config - SIDLE_SEQRECON found in conf/modules.config and Nextflow scripts.
• modules_config - SIDLE_TREERECON found in conf/modules.config and Nextflow scripts.
• modules_config - DECONTAM found in conf/modules.config and Nextflow scripts.
• modules_config - BARRNAP found in conf/modules.config and Nextflow scripts.
• modules_config - BARRNAPSUMMARY found in conf/modules.config and Nextflow scripts.
• modules_config - FILTER_SSU found in conf/modules.config and Nextflow scripts.
• modules_config - FILTER_LEN_ASV found in conf/modules.config and Nextflow scripts.
• modules_config - FILTER_CODONS found in conf/modules.config and Nextflow scripts.
• modules_config - MERGE_STATS_CUTADAPT found in conf/modules.config and Nextflow scripts.
• modules_config - ITSX_CUTASV found in conf/modules.config and Nextflow scripts.
• modules_config - ITSXRUST_CUTASV found in conf/modules.config and Nextflow scripts.
• modules_config - FILTER_LEN_ITSX found in conf/modules.config and Nextflow scripts.
• modules_config - FORMAT_TAXONOMY found in conf/modules.config and Nextflow scripts.
• modules_config - DADA2_TAXONOMY found in conf/modules.config and Nextflow scripts.
• modules_config - CONSOLIDATE_DADA2_TAXONOMY found in conf/modules.config and Nextflow scripts.
• modules_config - DADA2_ADDSPECIES found in conf/modules.config and Nextflow scripts.
• modules_config - FORMAT_TAXONOMY_SINTAX found in conf/modules.config and Nextflow scripts.
• modules_config - VSEARCH_SINTAX found in conf/modules.config and Nextflow scripts.
• modules_config - FORMAT_TAXRESULTS_SINTAX found in conf/modules.config and Nextflow scripts.
• modules_config - KRAKEN2_KRAKEN2 found in conf/modules.config and Nextflow scripts.
• modules_config - FORMAT_TAXRESULTS_KRAKEN2 found in conf/modules.config and Nextflow scripts.
• modules_config - VSEARCH_USEARCHGLOBAL found in conf/modules.config and Nextflow scripts.
• modules_config - VSEARCH_USEARCHGLOBAL_LCA found in conf/modules.config and Nextflow scripts.
• modules_config - FORMAT_TAXONOMY_VSEARCH_LCA found in conf/modules.config and Nextflow scripts.
• modules_config - FORMAT_TAXRESULTS_VSEARCH_LCA found in conf/modules.config and Nextflow scripts.
• modules_config - VSEARCH_CLUSTER found in conf/modules.config and Nextflow scripts.
• modules_config - FILTER_CLUSTERS found in conf/modules.config and Nextflow scripts.
• modules_config - ASSIGNSH found in conf/modules.config and Nextflow scripts.
• modules_config - FORMAT_TAXONOMY_QIIME found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_EXTRACT found in conf/modules.config and Nextflow scripts.
• modules_config - HMMER_HMMRANK found in conf/modules.config and Nextflow scripts.
• modules_config - HMMER_HMMBUILD found in conf/modules.config and Nextflow scripts.
• modules_config - HMMER_UNALIGNREF found in conf/modules.config and Nextflow scripts.
• modules_config - HMMER_HMMALIGNREF found in conf/modules.config and Nextflow scripts.
• modules_config - HMMER_HMMALIGNQUERY found in conf/modules.config and Nextflow scripts.
• modules_config - HMMER_MASK found in conf/modules.config and Nextflow scripts.
• modules_config - HMMER_MASKQUERY found in conf/modules.config and Nextflow scripts.
• modules_config - HMMER_MASKREF found in conf/modules.config and Nextflow scripts.
• modules_config - HMMER_AFAFORMATQUERY found in conf/modules.config and Nextflow scripts.
• modules_config - HMMER_AFAFORMATREF found in conf/modules.config and Nextflow scripts.
• modules_config - MAFFT found in conf/modules.config and Nextflow scripts.
• modules_config - CLUSTALO_ALIGN found in conf/modules.config and Nextflow scripts.
• modules_config - EPANG_PLACE found in conf/modules.config and Nextflow scripts.
• modules_config - GAPPA_GRAFT found in conf/modules.config and Nextflow scripts.
• modules_config - GAPPA_ASSIGN found in conf/modules.config and Nextflow scripts.
• modules_config - GAPPA_HEATTREE found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_INASV found in conf/modules.config and Nextflow scripts.
• modules_config - PPLACEFORMATTAX found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_INASV_BPAVG found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_TABLEFILTERTAXA found in conf/modules.config and Nextflow scripts.
• modules_config - FILTER_STATS found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_BARPLOT found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_BPAVG found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_EXPORT_ABSOLUTE found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_EXPORT_RELASV found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_TREE found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_FILTERSAMPLES_ANCOM found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_ALPHARAREFACTION found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_DIVERSITY_CORE found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_DIVERSITY_ALPHA found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_DIVERSITY_ADONIS found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_ANCOM_TAX found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_ANCOMBC_TAX found in conf/modules.config and Nextflow scripts.
• modules_config - ANCOMBC_FORMULA_TAX found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_ANCOMBC2_TAX found in conf/modules.config and Nextflow scripts.
• modules_config - ANCOMBC2_FORMULA_TAX found in conf/modules.config and Nextflow scripts.
• modules_config - PICRUST found in conf/modules.config and Nextflow scripts.
• modules_config - SBDIEXPORT found in conf/modules.config and Nextflow scripts.
• modules_config - SBDIEXPORTREANNOTATE found in conf/modules.config and Nextflow scripts.
• modules_config - PHYLOSEQ found in conf/modules.config and Nextflow scripts.
• modules_config - TREESUMMARIZEDEXPERIMENT found in conf/modules.config and Nextflow scripts.
• modules_config - VSEARCH_USEARCHGLOBAL_BM found in conf/modules.config and Nextflow scripts.
• modules_config - COMPARE_SEQUENCES found in conf/modules.config and Nextflow scripts.
• modules_config - COMPARE_PERFORMANCE found in conf/modules.config and Nextflow scripts.
• modules_config - COMPARE_PROFILE found in conf/modules.config and Nextflow scripts.
• modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
• modules_config - SUMMARY_REPORT found in conf/modules.config and Nextflow scripts.
• nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
• nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 4.1.0
• rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.
• container_configs - conf/containers_conda_lock_files_amd64.config is up to date
• container_configs - conf/containers_conda_lock_files_arm64.config is up to date
• container_configs - conf/containers_docker_amd64.config is up to date
• container_configs - conf/containers_docker_arm64.config is up to date
• container_configs - conf/containers_singularity_https_amd64.config is up to date
• container_configs - conf/containers_singularity_https_arm64.config is up to date
• container_configs - conf/containers_singularity_oras_amd64.config is up to date
• container_configs - conf/containers_singularity_oras_arm64.config is up to date

Run details

• nf-core/tools version 4.1.0
• Run at 2026-09-24 14:12:40

[github-actions]

❌ nf-test failed with latest Nextflow version

Note

Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
Please check if the failure is expected with newer (edge-)releases of Nextflow or if it needs fixing.

• ❌ docker | latest-everything | Shard 2/20

See the full run for details.

[d4straub]

Looks almost good to me. Two nitpicks:

• the fruitless execution of BUILD_ASV_ANNOTATIONS (details below)
• now that we have those summery_tables folder, maybe we should also store "overall_summary.tsv" there (and rename it to maybe something like read_counts_passed.tsv)?

[d4straub]

I saw in the .snap files that three tests execute BUILD_ASV_ANNOTATIONS but not SUMMARY_TABLE_TAXONOMY and produce no additional output. Additional module execution without benefit seems pointless. Maybe that could be avoided?

The three tests in question (with the settings that I suspect causing that):

• doubleprimers (skip_dada_taxonomy = true & kraken2_ref_taxonomy = "greengenes")
• multiregion (skip_dada_taxonomy = true & sidle_ref_taxonomy = "greengenes88")
• novaseq (skip_taxonomy = true)

[erikrikarddaniel]

Good catch, and you identified the right three.
BUILD_ASV_ANNOTATIONS is called unconditionally, but the only thing that reads its output is SUMMARY_TABLE_TAXONOMY, which consumes ch_tax_tsv with Kraken2 filtered out.
In all three of those profiles that filtered channel is empty -- Kraken2 only in doubleprimers, SIDLE never enters ch_tax_tsv in multiregion, and novaseq skips taxonomy altogether -- so the annotations get built and then dropped.

I would rather not gate it on the parameters, since ch_tax_tsv is filled from six separate places under six different conditions and a parameter expression would have to restate all of them, which is the maintenance trap you pointed at in the other thread.
Gating on the channel itself keeps the two in step:

ch_summary_tax = ch_tax_tsv.filter { meta, _tsv -> meta.classifier != "KRAKEN2" }

ch_annot_barrnap = ch_summary_tax
    .map { _meta, _tsv -> true }
    .first()
    .combine( ch_barrnapsummary.ifEmpty( [] ) )
    .map { _gate, summary -> summary }

The gated channel replaces the module's first input and the other twelve stay as they are, so the module itself does not change.
I checked the operator behaviour on its own before wiring it in: an empty taxonomy channel leaves the process unexecuted, and several taxonomy tables still run it exactly once.

I will push this and confirm the three snapshots lose the process without anything else moving.

[erikrikarddaniel]

Done in ecd0115.

BUILD_ASV_ANNOTATIONS now takes its first input through a gate derived from the channel SUMMARY_TABLE_TAXONOMY consumes, so it runs only when there is a taxonomy table to join the annotations onto.
The module itself is unchanged, and SUMMARY_TABLE_TAXONOMY reuses the same filtered channel rather than filtering a second time.

All three profiles you named now lose the module's entry from the versions file and nothing else moves in their snapshots:

• doubleprimers passed
• multiregion passed
• novaseq passed

fasta was run as a control, since it does write a summary table, and its snapshot is byte-identical.

[d4straub]

LGTM!