feat: remove MSstats post-processing step from quantms

[ypriverol]

Summary

• Removes MSSTATS_LFQ and MSSTATS_TMT modules and their R scripts (bin/msstats_plfq.R, bin/msstats_tmt.R, bin/msstats_utils.R) from the pipeline
• Removes all MSstats-specific parameters from nextflow.config and nextflow_schema.json (skip_post_msstats, ref_condition, contrasts, msstats_* params)
• Removes the MSstats publishDir block from conf/modules/shared.config
• Keeps MSSTATS_CONVERTER (OpenMS) and DIANN_MSSTATS so quantms still produces msstats_in.csv as input for downstream MSstats analysis
• Updates docs to clarify that users should run MSstats manually outside the pipeline

Motivation

MSstats post-processing is interactive and exploratory. Embedding it in the automated pipeline creates unnecessary complexity — users need to re-run with different contrasts or parameters. quantms should produce the MSstats-compatible input files and stop there, leaving statistical analysis to the user.

Closes #697 (if applicable)

Test plan

• Run test_lfq profile: verify quant_tables/msstats_in.csv is still produced
• Run test_tmt profile: verify quant_tables/out_msstats_in.csv is still produced
• Run test_dia profile: verify msstats_in.csv is still produced
• Verify msstats/ output directory is no longer created
• Verify nf-schema validation passes

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[Copilot]

Pull request overview

Removes the in-pipeline MSstats post-processing steps (R-based MSstats/MSstatsTMT execution) while keeping generation of MSstats-compatible input tables (*_msstats_in.csv) for downstream, user-run MSstats analysis.

Changes:

• Removed MSSTATS_LFQ / MSSTATS_TMT modules and their invocation from LFQ/TMT/DIA workflows.
• Removed MSstats post-processing parameters from nextflow.config and nextflow_schema.json, plus the dedicated msstats/ publishDir.
• Updated output documentation and test configs to reflect that MSstats is no longer run inside the pipeline.

Reviewed changes

Copilot reviewed 15 out of 18 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
workflows/tmt.nf	Drops MSSTATS_TMT step and stops emitting msstats_out.
workflows/lfq.nf	Drops MSSTATS_LFQ step and stops emitting msstats_out.
workflows/dia.nf	Drops MSSTATS_LFQ post-step and stops emitting msstats_out.
nextflow_schema.json	Removes MSstats post-processing parameter group and schema reference.
nextflow.config	Removes MSstats post-processing params defaults.
conf/modules/shared.config	Removes msstats/ publishDir block for MSstats post-processing outputs.
conf/tests/test_localize.config	Removes skip_post_msstats test param.
conf/tests/test_latest_dia.config	Removes skip_post_msstats test param.
conf/tests/test_dia_dotd.config	Removes skip_post_msstats test param.
conf/tests/test_dia.config	Removes skip_post_msstats test param.
docs/output.md	Updates output structure/docs to state MSstats is run externally.
modules/local/msstats/msstats_tmt/meta.yml	Deleted MSstatsTMT module metadata.
modules/local/msstats/msstats_tmt/main.nf	Deleted MSstatsTMT Nextflow process.
modules/local/msstats/msstats_lfq/meta.yml	Deleted MSstats LFQ module metadata.
modules/local/msstats/msstats_lfq/main.nf	Deleted MSstats LFQ Nextflow process.
bin/msstats_utils.R	Deleted shared MSstats R helper script.
bin/msstats_tmt.R	Deleted MSstatsTMT R runner script.
bin/msstats_plfq.R	Deleted MSstats LFQ R runner script.

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