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Improving doc #319

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merged 3 commits into from
Oct 30, 2023
Merged

Improving doc #319

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8b31b61
Update CHANGELOG.md
daichengxin Oct 30, 2023
0353f8f
improving doc
daichengxin Oct 30, 2023
105602e
Merge branch 'dev' into dev
ypriverol Oct 30, 2023
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6 changes: 4 additions & 2 deletions CHANGELOG.md
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Expand Up @@ -15,13 +15,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Changed`

- Update for pmultiqc to pmultiqc=0.0.21
- Update for openms to openms=3.1.0
- [#314](https://github.com/bigbio/quantms/pull/314) Update for pmultiqc to pmultiqc=0.0.23
- [#308](https://github.com/bigbio/quantms/pull/308) Update for openms to openms=3.1.0
- Update for sdrf-pipelines to sdrf-pipelines=0.0.24
- Update for msstats to msstats=4.2.1

### `Fixed`

- [#316](https://github.com/bigbio/quantms/pull/316) Fixed jar path selection of luciphoradapter and msgf+
- Fixed bug where modification masses were not calculated correctly in DIA-NN conversion.
- Fixed multiple bugs Pull Request [#293 BigBio](https://github.com/bigbio/quantms/pull/293), [#279 BigBio](https://github.com/bigbio/quantms/pull/279), [#265 BigBio](https://github.com/bigbio/quantms/pull/265), [#260 BigBio](https://github.com/bigbio/quantms/pull/260), [#257 BigBio](https://github.com/bigbio/quantms/pull/257)

Expand All @@ -36,6 +37,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- lfq_intensity_threshold: Minimum intensity of a feature to be considered in the MBR algorithm (default: 1000)
- sage_processes: Number of processes to use in SAGE search engine (default: 1)
- diann_speclib: Path to the spectral library to use in DIA-NN (default: null)
- convert_dotd: if convert .d file to mzml (default: false)

### `Deprecations`

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9 changes: 5 additions & 4 deletions README.md
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Expand Up @@ -55,10 +55,11 @@ On release, automated continuous integration tests run the pipeline on a full-si

### DIA-LFQ (data-independent label-free quantification)

1. RAW file conversion to mzML ([`thermorawfileparser`](https://github.com/compomics/ThermoRawFileParser))
2. DIA-NN analysis [`dia-nn`](https://github.com/vdemichev/DiaNN/)
3. Generation of output files (msstats)
4. QC reports generation [`pmultiqc`](https://github.com/bigbio/pmultiqc)
1. RAW file conversion to mzML when RAW as input([`thermorawfileparser`](https://github.com/compomics/ThermoRawFileParser))
2. Performing an [optional step](https://github.com/bigbio/quantms/blob/dev/modules/local/tdf2mzml/main.nf): Converting .d to mzML when bruker data as input and set `convert_dotd` to true
3. DIA-NN analysis [`dia-nn`](https://github.com/vdemichev/DiaNN/)
4. Generation of output files (msstats)
5. QC reports generation [`pmultiqc`](https://github.com/bigbio/pmultiqc)

### Functionality overview

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