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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.
vinisalazar
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nickp60
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Mar 6, 2026
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This is great, thanks! Thanks for implementing all possible cases for the tests
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Support and test SE reads (#12)
Summary of changes: