v1.2.0

Aligned with the nf-core tools v4.0.2 ruleset.

nf-module-dev

• research step now requires cross-checking official docs and the command's --help output, with explicit instruction to write down every mandatory + optional input file, every flag, and every possible output (no silent omissions)
• prefer a single input tuple (tuple val(meta), path(reads), path(reference), ...) over multiple separate channels — split only when inputs have genuinely different cardinalities
• emitted version string MUST be bare numeric (1.0.0) — no v prefix, no tool name, no commit hash; strip with sed/awk inside the eval
• added meta-map naming rules (meta, meta2, meta3); only meta.id and meta.single_end are accepted standard keys; pass extras via ext.args
• added args / args2 / args3 numbering rule for piped tools, by pipe position
• explicit rule to never modify the when: block — conditional execution belongs in process.ext.when in pipeline config
• prefer compressed output formats (*.fastq.gz over *.fastq, *.bam over *.sam) and use UNIX pipes to avoid intermediate writes
• scripts longer than ~20 lines must move to templates/<module>.<ext> rather than inline
• stub block for gzipped outputs must use echo "" | gzip > "${prefix}.txt.gz" — touch foo.txt.gz produces an empty file that breaks downstream parsers
• forced redirection 2>| instead of 2> (nf-core enables noclobber)
• hardcoded val('1.2.3') fallback documented for tools with no --version flag, with required explanatory comment
• consolidated all version-emission rules into a single ## Reference: versions output section to remove duplication between rules and example

nf-test-expert

• added priority-3 assertion option path(...).readLines().contains("<expected line>") between line-count and bare file-existence — keeps a content-level guarantee when full snapshots are unstable
• added singularity-pull failure fallback — when image pull fails, the agent now hands the user the exact singularity pull ... && mv ... command (with Nextflow cache-name conventions) instead of silently retrying or working around it
• documented the params.modules_testdata_base_path convention for referencing shared test data; ${projectDir} is now reserved for temporary module-local fixtures
• added empty-output rule — real (non-stub) tests must not snapshot the empty-file MD5 d41d8cd98f00b204e9800998ecf8427e; fix the test data or disregard that channel output completely
• explicit "stub test is mandatory" rule — every module needs at least one options "-stub" test as the minimum CI safety net
• documented .github/skip_nf_test.json (alphabetical) for legitimately unsupported profiles
• clarified that upstream-dependency tags (mmseqs, mmseqs/createdb etc. for setup-block runs) are mandatory because they cause upstream changes to re-trigger this module's CI

nf-secretary

• workflow now runs nextflow lint <main.nf> (strict Nextflow grammar check) before nf-core modules lint to catch syntax issues early
• EDAM lookup procedure added — agent must check the built-in table, then grep existing repo meta.yml files, then search the EDAM ontology directly, before settling for ontologies: []
• EDAM coverage rule made explicit — every file entry, input AND output, gets ontologies populated; no skipping after the first one
• reconciled prior guidance about --fix-inserted ontologies: [] — the agent now treats each as a TODO and runs the lookup procedure before leaving it empty
• added tools block requirements — every invoked tool listed individually, with args_id matching the $args / $args2 / $args3 numbering from main.nf
• keywords rule strengthened — must cover research domain / data type / function and MUST NOT be solely the (sub)tool name; multi-tool modules add the multi-tool keyword plus each component
• input-block rules expanded — tuple inputs split into separate entries, every meta map (meta, meta2, …) documented individually, each input marked Mandatory or Optional in its description, file pattern is Java glob syntax
• documented the type: whitelist (map, file, directory, string, boolean, integer, float, list) — anything else fails schema validation