pmultiqc 0.0.39 incompatible with pipeline CLI flags and OpenMS mzTab — SUMMARY_PIPELINE fails

[Cpennica]

Description of the bug

The pmultiqc step (SUMMARY_PIPELINE) does not produce a report on a standard LFQ-DDA run. The module pins pmultiqc:0.0.39 and passes MultiQC options with underscores, but pmultiqc ≥ 0.0.40 (MultiQC ≥ 1.33) renamed all plugin CLI options to hyphens. 0.0.39 also lacks guards for optional mzTab columns and for missing mzML statistics, so it crashes on the OpenMS mzTab this pipeline produces. Fixing one issue only reveals the next:

1. pmultiqc 0.0.39 — KeyError: '<run>' in parse_idxml (self.mzml_table[spectrum_name] = mzml_table[spectrum_name], no membership guard).
2. pmultiqc ≥ 0.0.40 — No such option: --quantms_plugin; the module also builds --disable_table, --ignored_idxml, --contaminant_affix, --quantification_method, --pmultiqc_version, all of which must be hyphenated.
3. pmultiqc 0.0.40 — KeyError: 'opt_global_q-value' in parse_out_mztab; OpenMS 2026.06.06 mzTab doesn't expose that column (guarded in newer pmultiqc).
4. pmultiqc 0.0.44 — KeyError: '<run>' in calculate_heatmap because mzml_statistics defaults to false, so no *_ms_info.parquet is generated and per-run heatmap scores are empty.

Fixes that produced a working run: bump the pmultiqc container to 0.0.44, hyphenate all pmultiqc CLI flags in modules/local/pmultiqc/main.nf (including --pmultiqc-version in the versions block), and set mzml_statistics = true.

Command used and terminal output

Relevant files

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System information

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