Version 1.2 [PLEASE DO NOT MERGE YET]

.devcontainer/devcontainer.json

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

.editorconfig

@@ -8,7 +8,7 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
-[*.{md,yml,yaml,html,css,scss,js,cff}]
+[*.{md,yml,yaml,html,css,scss,js}]
 indent_size = 2
 
 # These files are edited and tested upstream in nf-core/modules

.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
 
@@ -116,4 +118,3 @@ To get started:
 Devcontainer specs:
 
 - [DevContainer config](.devcontainer/devcontainer.json)
-- [Dockerfile](.devcontainer/Dockerfile)

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -42,9 +42,9 @@ body:
     attributes:
       label: System information
       description: |
-        * Nextflow version _(eg. 22.10.1)_
+        * Nextflow version _(eg. 23.04.0)_
         * Hardware _(eg. HPC, Desktop, Cloud)_
         * Executor _(eg. slurm, local, awsbatch)_
-        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
         * Version of nf-core/quantms _(eg. 1.1, 1.5, 1.8.2)_

.github/workflows/awsfulltest.yml

@@ -19,23 +19,24 @@ jobs:
         mode: ["lfq", "tmt", "dia"]
     steps:
       - name: Launch workflow via tower
-        uses: nf-core/tower-action@v3
+        uses: seqeralabs/action-tower-launch@v2
 
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/quantms/work-${{ github.sha }}
           parameters: |
             {
+              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/quantms/results-${{ github.sha }}/mode_${{ matrix.mode }}"
             }
+          profiles: test_${{ matrix.mode }}
 
-          profiles: test_${{ matrix.mode }},aws_tower
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
-          path: tower_action_*.log
-          nextflow_config: |
-            process.errorStrategy = 'retry'
-            process.maxRetries = 3
+          path: |
+            tower_action_*.log
+            tower_action_*.json

.github/workflows/awstest.yml

@@ -12,21 +12,22 @@ jobs:
     steps:
       # Launch workflow using Tower CLI tool action
       - name: Launch workflow via tower
-        uses: nf-core/tower-action@v3
+        uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/quantms/work-${{ github.sha }}
           parameters: |
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/quantms/results-test-${{ github.sha }}"
             }
-          profiles: test_tmt,aws_tower
+          profiles: test_tmt
+
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
-          path: tower_action_*.log
-          nextflow_config: |
-            process.errorStrategy = 'retry'
-            process.maxRetries = 3
+          path: |
+            tower_action_*.log
+            tower_action_*.json

.github/workflows/branch.yml

@@ -13,7 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == 'nf-core/quantms'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/quantms ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/quantms ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # If the above check failed, post a comment on the PR explaining the failure
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets

.github/workflows/ci.yml

@@ -32,9 +32,9 @@ jobs:
       matrix:
         # Nextflow versions
         NXF_VER:
-          - "22.10.1"
+          - "23.04.0"
           - "latest-everything"
-        test_profile: ["test_lfq", "test_dia", "test_localize", "test_tmt"]
+        test_profile: ["test_lfq", "test_lfq_sage", "test_dia", "test_localize", "test_tmt"]
         exec_profile: ["docker", "conda"]
         exclude:
           - test_profile: test_dia

.github/workflows/clean-up.yml

@@ -0,0 +1,24 @@
+name: "Close user-tagged issues and PRs"
+on:
+  schedule:
+    - cron: "0 0 * * 0" # Once a week
+
+jobs:
+  clean-up:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    steps:
+      - uses: actions/stale@v7
+        with:
+          stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
+          stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
+          close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity."
+          days-before-stale: 30
+          days-before-close: 20
+          days-before-pr-close: -1
+          any-of-labels: "awaiting-changes,awaiting-feedback"
+          exempt-issue-labels: "WIP"
+          exempt-pr-labels: "WIP"
+          repo-token: "${{ secrets.GITHUB_TOKEN }}"

.github/workflows/linting.yml

@@ -78,7 +78,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.7"
+          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 +12,9 @@ testing*
 /build/
 results*/
 venv/
+node_modules
+conversion_inputs
+debug_dir
+test_out
+
+lint_log.txt

.gitpod.yml

@@ -1,4 +1,9 @@
 image: nfcore/gitpod:latest
+tasks:
+  - name: Update Nextflow and setup pre-commit
+    command: |
+      pre-commit install --install-hooks
+      nextflow self-update
 
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack

.pre-commit-config.yaml

@@ -0,0 +1,5 @@
+repos:
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v2.7.1"
+    hooks:
+      - id: prettier

CHANGELOG.md

@@ -3,7 +3,45 @@
 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).
 
-## [1.1.1] nfcore/quantms - [TBD] - Berlin-Bern
+## [1.2.0dev] nfcore/quantms - [TBD] - Thimphu
+
+### `Added`
+
+- [#275 BigBio](https://github.com/bigbio/quantms/pull/275) Added support for bruker data in DIA branch.
+- [#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`
+
+- [#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)
+
+### `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)
+- convert_dotd: if convert .d file to mzml (default: false)
+
+### `Deprecations`
+
+## [1.1.1] nfcore/quantms - [03/27/23] - Berlin-Bern
 
 ### `Added`
 

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.
@@ -47,8 +69,13 @@
   > The M, Käll L. Integrated Identification and Quantification Error Probabilities for Shotgun Proteomics. Mol Cell Proteomics. 2019 Mar;18(3):561-570. doi: 10.1074/mcp.RA118.001018. Epub 2018 Nov 27. PMID: 30482846; PMCID: PMC6398204.
 
 - [luciphor](https://pubmed.ncbi.nlm.nih.gov/23918812/)
+
   > Fermin D, Walmsley SJ, Gingras AC, Choi H, Nesvizhskii AI. LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach. Mol Cell Proteomics. 2013 Nov;12(11):3409-19. doi: 10.1074/mcp.M113.028928. Epub 2013 Aug 5. PMID: 23918812; PMCID: PMC3820951.
 
+- [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.
+
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)
@@ -65,5 +92,8 @@
 
 - [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
 
+  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.
+
 - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
+
   > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.