Dev#88
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Agent-Logs-Url: https://github.com/bigbio/quantms/sessions/65fad332-d4b1-4296-a973-d1593c808db4 Co-authored-by: ypriverol <52113+ypriverol@users.noreply.github.com>
…json Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…step Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Removes workflows/dia.nf and the entire modules/local/diann/ tree. DIA analysis is now handled by the dedicated quantmsdiann pipeline: https://github.com/bigbio/quantmsdiann Closes #697
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
DIA workflow has been moved to the dedicated quantmsdiann pipeline (https://github.com/bigbio/quantmsdiann). Updated README, output docs, and citations to reflect this change. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
….yml Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
- Keep deletion of conf/tests/test_full_dia.config and test_latest_dia.config (modified in dev but we are removing DIA support entirely) - Remove min_pr_mz/max_pr_mz/min_fr_mz/max_fr_mz from nextflow_schema.json (re-added in dev for DIA-NN, not needed after workflow removal) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Add `|| echo "unknown"` so versions.yml gets a safe value if the bundled executable path ever changes between container rebuilds, rather than an empty/broken entry. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Fix filename pattern: msstats_in.csv -> *_msstats_in.csv (prefix is workflow-dependent) - Fix file type: TSV -> CSV (actual output is comma-separated) - Rename misleading "MSstats-processed mzTab" heading to "MSstats post-processing (external)" - Limit DDA pipelines to LFQ and ISO (DIA removed) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Add a second defensive check for dia acquisition_method before the label-free branching, with a clear error message pointing users to https://github.com/bigbio/quantmsdiann. Addresses reviewer comment from enryH on PR #702. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
feat: remove DIA-NN workflow, redirect to quantmsdiann
- Accept deletion of DIA files (dia.nf, test_dia*.config) merged via PR #702 - shared.config: remove MSSTATS_LFQ|MSSTATS_TMT publishDir block (our change) and FINAL_QUANTIFICATION|DIANN_MSSTATS from quant_tables pattern (from dev) - nextflow_schema.json: remove both DIA-NN and statistical_post_processing $defs blocks and their allOf $refs (each PR removed one; merged = remove both) - docs/output.md: remove DIA output structure sections (from dev) and MSstats-processed results entry (our change); keep improved MSstats description with correct filename pattern and CSV type Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
With Nextflow's set -euo pipefail, the || operator inside $() does not
behave reliably when a pipeline fails: the subshell exits early (set -e),
leaving $() empty, and echo "unknown" leaks into the heredoc as a bare
word, producing invalid YAML ("unknown" without a colon on its own line).
Dropping the fallback is safe because:
- The correct binary path is already the real fix (comet was not on PATH)
- /opt/OpenMS/thirdparty/Comet/comet.exe exists and produces the version
- An empty YAML value is valid if the command ever fails
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…-pmultiqc Fix Comet version reporting in pmultiqc software table
…sing feat: remove MSstats post-processing step from quantms
Drop the `by_sample` and `by_project` branches of `ms2features_range` together with the `IDRipper` Nextflow module. These modes exist only to enable a merged Percolator run that is then split back per-run for ConsensusID, which is not the direction the pipeline is heading. With the default `independent_run` path being the only supported topology, the three-way switch in `psm_rescoring`, `dda_id`, and `peptide_database_search` collapses to a single Percolator call per file. IDRipper remains available as a binary inside the OpenMS container (Sage's module still uses it internally for multi-file search output splitting), but the Nextflow module is deleted as it has no remaining caller. GET_SAMPLE / `extract_sample` is also removed — it existed solely to key the by_sample merge and has no other use. IDMerger's `ms2features_range`-keyed prefix logic is stripped (the module is kept for future reuse). Config surface shrinks: `ms2features_range` is removed from `nextflow.config` and `nextflow_schema.json`. `ms2features_enable` remains as the sole rescoring gate. No behaviour change for users on the default (`independent_run`). Anyone running with `by_sample` or `by_project` today will see a schema error on the removed parameter and will need to drop it from their config.
Two comments from the Copilot reviewer: 1. PSM_RESCORING still declared ch_file_preparation_results and _ch_expdesign in its take: block, but neither is used after the rescoring collapse. Dropped both from the workflow signature and updated the caller in subworkflows/local/id/main.nf. 2. The ms2features_range schema removal is a hard break, but nf-schema 2.5.1 only emits a warning for unknown parameters by default — so a config that still sets ms2features_range would be silently ignored rather than rejected. Added an explicit check in validateInputParameters() that errors with a migration message, and a new tests/removed_params.nf.test nf-test that asserts the pipeline fails with 'ms2features_range ... has been removed' when the parameter is provided.
The pipeline-test CI checker requires every nf.test to snapshot a versions.yml file, which a negative test (pipeline expected to fail) doesn't produce. The explicit rejection in validateInputParameters() still catches the removed ms2features_range parameter at runtime with a migration message; the nf-test wrapper isn't needed for that to work.
chore: remove ms2features_range modes and IDRipper
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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).