docs: drop stale diann_extra_args references (use extra_args)

The parameter was renamed to 'extra_args', but the worked example in
docs/usage.md still used the old 'diann_extra_args' name. That name is no
longer read by the pipeline, so it is silently ignored — flags like
--smart-profiling/--peak-center were dropped without warning. Update the
example to 'extra_args' and remove the lingering 'formerly diann_extra_args'
note from conf/modules/dia.config. Passing 'diann_extra_args' is now flagged
by nf-schema as an unrecognised parameter rather than silently doing nothing.

Author: ypriverol

CHANGELOG.md

@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
+- Removed the stale `diann_extra_args` references. The parameter was renamed to `extra_args`, but the documented worked example still used the old name — which is silently ignored, so flags such as `--smart-profiling`/`--peak-center` were dropped. The worked example now uses `extra_args`, and passing `diann_extra_args` is flagged by nf-schema parameter validation as unrecognised. Use `extra_args` (or, better, the dedicated parameters where they exist).
 - Documentation: clarified DIA-NN container licensing. Only DIA-NN 1.8.1 is publicly redistributable (pulled from BioContainers as the default); releases from 1.9 onward must be built locally from the [quantms-containers](https://github.com/bigbio/quantms-containers) recipes and tagged `ghcr.io/bigbio/diann:<version>` so the matching `-profile diann_v<version>` resolves them. Added the missing DIA-NN 2.5.0 row to the README support table.
 - QPX export now publishes the Parquet dataset files and the `.h5mu` MuData file directly under `results/qpx/`, removing the intermediate `qpx/qpx_output/` subfolder. The `bigbio/qpx` module emits the dataset as `qpx_output/*` files (bigbio/nf-modules#39) so `publishDir` can flatten them.
 - `--precursor_qvalue` default is now **version-aware**: unset resolves by `--diann_version` to `0.01` (1%) for DIA-NN < 2.5 and `0.05` (5%) for >= 2.5, matching DIA-NN's recommended precursor q-value. An explicit `--precursor_qvalue` always overrides and is never replaced by the version default. Applies to both the DIA-NN main report (`--qvalue`) and the MSstats input; the matrix thresholds (`--matrix_qvalue`, `--matrix_spec_q`) are unchanged.

conf/modules/dia.config

@@ -2,7 +2,7 @@
 ========================================================================================
     DIA-NN module options — all DIA pipeline steps
 ========================================================================================
-    Passes params.extra_args (formerly params.diann_extra_args) to each DIA-NN step via ext.args.
+    Passes params.extra_args to each DIA-NN step via ext.args.
     Blocked-flag validation is performed in each module's script block,
     so it applies regardless of whether ext.args is overridden by the user.
 ----------------------------------------------------------------------------------------

docs/usage.md

@@ -431,7 +431,7 @@ mass_acc_automatic: false # GUI used fixed tolerances; required for Bruker timsT
 mass_acc_ms1: 15
 mass_acc_ms2: 15
 pg_level: 2
-diann_extra_args: "--smart-profiling --peak-center"
+extra_args: "--smart-profiling --peak-center"
 ```
 
 ### Common pitfalls