Merge pull request #293 from jonasscheid/add_ms2rescore

Add ms2rescore module, remove ms2pip and deeplc modules

.github/workflows/awsfulltest.yml

@@ -15,9 +15,6 @@ jobs:
     steps:
       - name: Launch workflow via tower
         uses: seqeralabs/action-tower-launch@v2
-        # TODO nf-core: You can customise AWS full pipeline tests as required
-        # Add full size test data (but still relatively small datasets for few samples)
-        # on the `test_full.config` test runs with only one set of parameters
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

.github/workflows/ci.yml

@@ -55,7 +55,7 @@ jobs:
           # Test latest edge release of Nextflow
           - NXF_VER: ""
             NXF_EDGE: "1"
-        tests: ["test_deeplc", "test_ms2pip", "test_ionannotator", "test_full"]
+        tests: ["test_mokapot", "test_percolator", "test_ionannotator"]
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2

CHANGELOG.md

@@ -3,6 +3,16 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v2.6.0dev - nfcore/mhcquant
+
+### `Added`
+
+- Adding MS²Rescore module with the underlying python CLI [#288](https://github.com/nf-core/mhcquant/issues/288)
+
+### `Deprecated`
+
+- Removed MS²PIP and DeepLC modules. These feature generators are now called via the MS²Rescore framework
+
 ## v2.5.0 - nfcore/mhcquant "Angry Bird" - 2023/10/09
 
 ### `Added`

CITATIONS.md

@@ -10,9 +10,41 @@
 
 ## Pipeline tools
 
+- [OpenMS](https://pubmed.ncbi.nlm.nih.gov/27575624/)
+
+  > Röst H, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, Rurik M, Schmitt U, Veit J, Walze M, Wojnar D, Wolski WE, Schilling O, Choudhary JS, Malmström L, Aebersold R, Reinert K, Kohlbacher O. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Methods 13 741–748 (2016). doi: 10.1038/nmeth.3959. PubMed PMID: 27575624
+
+- [Comet](https://pubmed.ncbi.nlm.nih.gov/26115965/)
+
+  > Eng JK, Hoopmann MR, Jahan TA, Egertson JD, Noble WS, MacCoss MJ. A Deeper Look into Comet—Implementation and Features. Journal of the American Society for Mass Spectrometry 26,11 1865-1874 (2015). doi: 10.1007/s13361-015-1179-x. PMID: 26115965
+
+- [DeepLC](https://pubmed.ncbi.nlm.nih.gov/34711972/)
+
+  > Bouwmeester R, Gabriels R, Hulstaert N, Martens L, Degroeve S. DeepLC can predict retention times for peptides that carry as-yet unseen modifications. Nature Methods 18,11 1363-1369 (2021). doi:1 0.1038/s41592-021-01301-5. PMID: 34711972
+
+- [MS²PIP](https://pubmed.ncbi.nlm.nih.gov/31028400/)
+
+  > Gabriels R, Martens L, Degroeve S. Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques. Nucleic Acids Res. 2019 Jul 2;47(W1):W295-W299. doi: 10.1093/nar/gkz299. PMID: 31028400; PMCID: PMC6602496.
+
+- [MS²Rescore](https://pubmed.ncbi.nlm.nih.gov/35803561/)
+
+  > Declercq A, Bouwmeester R, Hirschler A, Carapito C, Degroeve S, Martens L, Gabriels R. MS²Rescore: Data-Driven Rescoring Dramatically Boosts Immunopeptide Identification Rates. Mol Cell Proteomics. 2022 Aug;21(8):100266. doi: 10.1016/j.mcpro.2022.100266. Epub 2022 Jul 6. PMID: 35803561; PMCID: PMC9411678.
+
+- [Ionmob](https://pubmed.ncbi.nlm.nih.gov/37540201/)
+
+  > Teschner D, Gomez-Zepeda D, Declercq A, Łącki MK, Avci S, Bob K, Distler U, Michna T, Martens L, Tenzer S, Hildebrandt A. Ionmob: a Python package for prediction of peptide collisional cross-section values. Bioinformatics. 2023 Sep 2;39(9):btad486. doi: 10.1093/bioinformatics/btad486. PMID: 37540201; PMCID: PMC10521631.
+
+- [Percolator](https://pubmed.ncbi.nlm.nih.gov/31407580/)
+
+  > Halloran JT, Zhang H, Kara K, Renggli C, The M, Zhang C, Rocke DM, Käll L, Noble WS. Speeding Up Percolator. J Proteome Res. 2019 Sep 6;18(9):3353-3359. doi: 10.1021/acs.jproteome.9b00288. Epub 2019 Aug 23. PMID: 31407580; PMCID: PMC6884961.
+
+- [Mokapot](https://pubmed.ncbi.nlm.nih.gov/33596079/)
+
+  > Fondrie WE, Noble WS. mokapot: Fast and Flexible Semisupervised Learning for Peptide Detection. J Proteome Res. 2021 Apr 2;20(4):1966-1971. doi: 10.1021/acs.jproteome.0c01010. Epub 2021 Feb 17. PMID: 33596079; PMCID: PMC8022319.
+
 - [FRED2](https://pubmed.ncbi.nlm.nih.gov/27153717/)
 
-  > Schubert B, WalzerM, Brachvogel HP, Szolek A, Mohr C, Kohlbacher O, FRED 2: an immunoinformatics framework for Python, Bioinformatics, Volume 32, Issue 13, 1 July 2016, Pages 2044–2046. doi: 10.109 bioinformatics/btw113. PubMed PMID: 27153717; PubMed Central PMCID; PMC4920123.
+  > Schubert B, WalzerM, Brachvogel HP, Szolek A, Mohr C, Kohlbacher O, FRED 2: an immunoinformatics framework for Python, Bioinformatics, Volume 32, Issue 13, 1 July 2016, Pages 2044–2046. doi: 10.1093/bioinformatics/btw113. PubMed PMID: 27153717; PubMed Central PMCID; PMC4920123.
 
 - [MHCflurry](https://pubmed.ncbi.nlm.nih.gov/27153717/)
 
@@ -22,10 +54,6 @@
 
   > Shao XM, Bhattacharya R, Huang J, Sivakumar IKA, Tokheim C, Zheng L, Hirsch D, Kaminow B, Omdahl A, Bonsack M, Riemer AB, Velculescu VE, Anagnostou V, Pagel KA, Karchin R. High-Throughput Prediction of MHC Class I and II Neoantigens with MHCnuggets. Cancer Immunol Res. 2020 Mar;8(3):396-408. doi: 10.1158/2326-6066.CIR-19-0464. Epub 2019 Dec 23. PMID: 31871119; PMCID: PMC7056596.
 
-- [OpenMS](https://pubmed.ncbi.nlm.nih.gov/27575624/)
-
-  > Röst H, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, Rurik M, Schmitt U, Veit J, Walze M, Wojnar D, Wolski WE, Schilling O, Choudhary JS, Malmström L, Aebersold R, Reinert K, Kohlbacher O. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Methods 13 741–748 (2016). doi: 10.1038/nmeth.3959. PubMed PMID: 27575624
-
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
   > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

README.md

@@ -1,7 +1,7 @@
 # ![nf-core/mhcquant](docs/images/nf-core-mhcquant_logo_light.png#gh-light-mode-only) ![nf-core/mhcquant](docs/images/nf-core-mhcquant_logo_dark.png#gh-dark-mode-only)
 
 [![GitHub Actions CI Status](https://github.com/nf-core/mhcquant/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/mhcquant/actions?query=workflow%3A%22nf-core+CI%22)
-[![GitHub Actions Linting Status](https://github.com/nf-core/mhcquant/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/mhcquant/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/mhcquant/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
+[![GitHub Actions Linting Status](https://github.com/nf-core/mhcquant/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/mhcquant/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/mhcquant/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.8427707-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.8427707)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
@@ -175,7 +175,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-If you use nf-core/mhcquant for your analysis, please cite it using the following doi: [10.5281/zenodo.1569909](https://doi.org/10.5281/zenodo.1569909) and the corresponding manuscript:
+If you use nf-core/mhcquant for your analysis, please cite it using the following doi: [10.5281/zenodo.8427707](https://doi.org/10.5281/zenodo.8427707) and the corresponding manuscript:
 
 > **MHCquant: Automated and Reproducible Data Analysis for Immunopeptidomics**
 >

assets/multiqc_config.yml

@@ -3,9 +3,9 @@ custom_logo_url: https://github.com/nf-core/mhcquant
 custom_logo_title: "nf-core/mhcquant"
 
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/mhcquant/releases/tag/2.5.0" target="_blank">nf-core/mhcquant</a>
+  This report has been generated by the <a href="https://github.com/nf-core/mhcquant/releases/tag/dev" target="_blank">nf-core/mhcquant</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/mhcquant/2.5.0/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/mhcquant/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-mhcquant-methods-description":
     order: -1000