Merge pull request #118 from bigbio/dev

Major PR for version 1.2 of quantms

.devcontainer/devcontainer.json

@@ -2,6 +2,7 @@
     "name": "nfcore",
     "image": "nfcore/gitpod:latest",
     "remoteUser": "gitpod",
+    "runArgs": ["--privileged"],
 
     // Configure tool-specific properties.
     "customizations": {

.github/CONTRIBUTING.md

@@ -9,7 +9,9 @@ Please use the pre-filled template to save time.
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
-> If you need help using or modifying nf-core/quantms then the best place to ask is on the nf-core Slack [#quantms](https://nfcore.slack.com/channels/quantms) channel ([join our Slack here](https://nf-co.re/join/slack)).
+:::info
+If you need help using or modifying nf-core/quantms then the best place to ask is on the nf-core Slack [#quantms](https://nfcore.slack.com/channels/quantms) channel ([join our Slack here](https://nf-co.re/join/slack)).
+:::
 
 ## Contribution workflow
 

.github/workflows/linting.yml

@@ -78,7 +78,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.8"
+          python-version: "3.11"
           architecture: "x64"
 
       - name: Install dependencies

.github/workflows/release-announcments.yml

@@ -0,0 +1,68 @@
+name: release-announcements
+# Automatic release toot and tweet anouncements
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  toot:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: rzr/fediverse-action@master
+        with:
+          access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
+          host: "mstdn.science" # custom host if not "mastodon.social" (default)
+          # GitHub event payload
+          # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release
+          message: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+
+  send-tweet:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: pip install tweepy==4.14.0
+      - name: Send tweet
+        shell: python
+        run: |
+          import os
+          import tweepy
+
+          client = tweepy.Client(
+              access_token=os.getenv("TWITTER_ACCESS_TOKEN"),
+              access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"),
+              consumer_key=os.getenv("TWITTER_CONSUMER_KEY"),
+              consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"),
+          )
+          tweet = os.getenv("TWEET")
+          client.create_tweet(text=tweet)
+        env:
+          TWEET: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+          TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }}
+          TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }}
+          TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }}
+          TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}
+
+  bsky-post:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: zentered/bluesky-post-action@v0.0.2
+        with:
+          post: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+        env:
+          BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }}
+          BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }}
+          #

.gitignore

@@ -12,3 +12,4 @@ testing*
 /build/
 results*/
 venv/
+lint_log.txt

CHANGELOG.md

@@ -7,14 +7,36 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#275 BigBio](https://github.com/bigbio/quantms/pull/275) Added support for bruker data.
+- [#275 BigBio](https://github.com/bigbio/quantms/pull/275) And speed-up to DIA-NN pipeline.
+- [#275 BigBio](https://github.com/bigbio/quantms/pull/275) Support for library-base search in DIA-NN pipeline.
+- [#300 BigBio](https://github.com/bigbio/quantms/pull/300) Major refactoring of LFQ-DDA MBR algorithm.
+- [#279 BigBio](https://github.com/bigbio/quantms/pull/279) Support for SAGE search engine.
+
 ### `Changed`
 
+- Update for pmultiqc to pmultiqc=0.0.21
+- 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`
 
+- 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)
+
 ### `Dependencies`
 
+- New dependency on `sage` search engine.
+
 ### `Parameters`
 
+- feature_with_id_min_score: Minimum score of a feature with a peptide identification (default: 0.10)
+- feature_without_id_min_score: Minimum score of a feature without peptide identification (transfer feature, default: 0.75)
+- 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)
+
 ### `Deprecations`
 
 ## [1.1.1] nfcore/quantms - [03/27/23] - Berlin-Bern

CITATIONS.md

@@ -1,5 +1,23 @@
 # nf-core/quantms: Citations
 
+## [Pipeline](https://www.researchsquare.com/article/rs-3002027/v1)
+
+> Chengxin Dai, Julianus Pfeuffer, Hong Wang et al. quantms: A cloud-based pipeline for proteomics reanalysis enables the quantification of 17521 proteins in 9,502 human samples., 01 June 2023, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-3002027/v1]
+
+## Pipeline research manuscripts
+
+- [proteogenomics](https://pubmed.ncbi.nlm.nih.gov/34904638/)
+
+  > Umer HM, Audain E, Zhu Y, Pfeuffer J, Sachsenberg T, Lehtiö J, Branca RM, Perez-Riverol Y. Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides. Bioinformatics. 2022 Feb 7;38(5):1470-1472. doi: 10.1093/bioinformatics/btab838. PMID: 34904638; PMCID: PMC8825679.
+
+- [lfq dda benchmark](https://pubmed.ncbi.nlm.nih.gov/37220883/)
+
+  > Bai M, Deng J, Dai C, Pfeuffer J, Sachsenberg T, Perez-Riverol Y. LFQ-Based Peptide and Protein Intensity Differential Expression Analysis. J Proteome Res. 2023 Jun 2;22(6):2114-2123. doi: 10.1021/acs.jproteome.2c00812. Epub 2023 May 23. PMID: 37220883; PMCID: PMC10243145.
+
+- [tissue absolute expression](https://pubmed.ncbi.nlm.nih.gov/37488995/)
+
+  > Wang H, Dai C, Pfeuffer J, Sachsenberg T, Sanchez A, Bai M, Perez-Riverol Y. Tissue-based absolute quantification using large-scale TMT and LFQ experiments. Proteomics. 2023 Jul 24:e2300188. doi: 10.1002/pmic.202300188. Epub ahead of print. PMID: 37488995.
+
 ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
 
 > Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.
@@ -38,6 +56,10 @@
 
   > Kim S., Pevzner PA. (2014). MS-GF+ makes progress towards a universal database search tool for proteomics. Nature communications, 5, 5277. doi: 10.1038/ncomms6277. PubMed PMID: 25358478; PubMed Central PMCID: PMC5036525
 
+- [Sage](https://pubmed.ncbi.nlm.nih.gov/37819886/)
+
+  > Lazear MR. Sage: An Open-Source Tool for Fast Proteomics Searching and Quantification at Scale. J Proteome Res. 2023 Oct 11. doi: 10.1021/acs.jproteome.3c00486. Epub ahead of print. PMID: 37819886.
+
 - [Epifany](https://pubmed.ncbi.nlm.nih.gov/31975601/)
 
   > Pfeuffer J, Sachsenberg T, Dijkstra TMH, Serang O, Reinert K, Kohlbacher O. EPIFANY: A Method for Efficient High-Confidence Protein Inference. J Proteome Res. 2020 Mar 6;19(3):1060-1072. doi: 10.1021/acs.jproteome.9b00566. Epub 2020 Feb 13. PMID: 31975601; PMCID: PMC7583457.