Release 1.0.0 (dev branch)#52
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- Don't use references to 'master' branch
- Add new stub tests to humann/regroup and humann/renorm modules - Run test profile in stub mode
CAT_FASTQ emits a bare path while the skip branch emits a list; normalize both to a list so downstream consumers don't need to handle both forms.
Tools that cannot handle paired-end input (humann_v3, humann_v4, fmhfunprofiler) now raise an explicit error if they receive more than one file, which would indicate CONCAT_ALL failed to produce a single concatenated FASTQ.
Add a validation step in prepareInputs for PE-aware tools that checks the number of read files matches meta.single_end (1 for SE, 2 for PE), so mismatches are caught early with a clear error message. Also document the expected channel structure so future tools added to this branch know they must use meta.single_end to switch CLI argument style.
Tests cover all four input scenarios (SE single-run, PE single-run, SE multi-run, PE multi-run) and verify that every code path produces a consistent [meta, [reads]] output structure with exactly one file, matching the normalization fix applied to the skip branch. Also verifies that multiple samples stay independent.
…sertions nf-test exposes channel path elements as Strings, not java.nio.Path/File objects, so .name raises MissingPropertyException. Use .endsWith() directly.
- Update docs and schemas accordingly
Get linting to pass
Improve docs
Draft conda envs for humann modules
Support and test single reads
feat: add module diamond/blastx from nf-core
Bugfixes and regrouping for ec comparisons between humann and mifaser
Docs fixes
Add tool citation text and enable MultiQC methods description
Keep current HEAD changes throughout; combine where incoming only adds (latest-everything NXF_VER in nf-test.yml, stable_path/stable_content variables in default.nf.test, multiqc/multiqc_logo/outdir take params in funcprofiler.nf). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- humann/humann4: rename duplicate `meta` input to `_meta` - profile: rename rgi_inputs to ch_input_for_rgi, add ch_input_for_eggnogmapper, fix shadowed `reads`/`profile` closure params to use underscore prefix - funcprofiler.nf: remove top-level statements (redundant, samplesheet/databases passed as workflow inputs) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Code review for #52
Applying fixes after running 'nf-core modules lint' command
- Remove action files while migration to v4 is not stable
- Code review for #52
Important! Template update for nf-core/tools v4.0.2 (fixing conflicts)
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Investigating RGI test problem
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).