Rearrange quant and prepare for release 2.5.0

.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/mhcquant then the best place to ask is on the nf-core Slack [#mhcquant](https://nfcore.slack.com/channels/mhcquant) channel ([join our Slack here](https://nf-co.re/join/slack)).
+:::info
+If you need help using or modifying nf-core/mhcquant then the best place to ask is on the nf-core Slack [#mhcquant](https://nfcore.slack.com/channels/mhcquant) channel ([join our Slack here](https://nf-co.re/join/slack)).
+:::
 
 ## Contribution workflow
 

.github/workflows/ci.yml

@@ -37,27 +37,37 @@ jobs:
 
       - name: Run pipeline with test data
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --spectrum_batch_size 5000 --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
 
-  test_additional_params:
-    name: Run pipeline with additional params
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mhcquant') }}"
+  profile:
+    name: Run profile tests
+    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mhcquant') }}
     runs-on: ubuntu-latest
+    env:
+      NXF_VER: ${{ matrix.nxf_ver }}
+      NXF_ANSI_LOG: false
     strategy:
       matrix:
-        NXF_VER:
-          - "23.04.0"
-          - "latest-everything"
+        include:
+          # Test pipeline minimum Nextflow version
+          - NXF_VER: "23.04.0"
+            NXF_EDGE: ""
+          # Test latest edge release of Nextflow
+          - NXF_VER: ""
+            NXF_EDGE: "1"
+        tests: ["test_deeplc", "test_ms2pip", "test_ionannotator", "test_quant", "test_full"]
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
-
+        uses: actions/checkout@v2
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
-        with:
-          version: "${{ matrix.NXF_VER }}"
-
-      - name: Run pipeline with additional params
+        env:
+          NXF_VER: ${{ matrix.NXF_VER }}
+          # Uncomment only if the edge release is more recent than the latest stable release
+          # See https://github.com/nextflow-io/nextflow/issues/2467
+          # NXF_EDGE: ${{ matrix.NXF_EDGE }}
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+      - name: Run pipeline with profile ${{ matrix.tests }}
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --predict_class_1 --predict_class_2 --predict_RT --spectrum_batch_size 2000 --use_deeplc --use_ms2pip --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.tests }},docker --max_memory '6.GB' --max_cpus 2 --spectrum_batch_size 5000 --outdir ./results

.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/[email protected]
+        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 }}
+          #

CHANGELOG.md

@@ -3,30 +3,34 @@
 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).
 
-## v2.4.2dev - [date]
+## v2.5.0 - nfcore/mhcquant "Angry Bird" - 2023/10/04
 
 ### `Added`
 
 - Support for brukers tdf format by adding tdf2mzml converter [#263](https://github.com/nf-core/mhcquant/issues/263)
 - DeepLC retention time prediction
 - MS2PIP peak intensity prediction
-- Added OpenMS FileFilter to clean mzml after parsing to remove artifacts like empty spectra or precursors with charge 0
+- Added OpenMS FileFilter to clean mzml after parsing to remove artifacts like empty spectra or precursors with charge 0 (optional)
 - Made file extension check case insensitive
 - Added option to provide a default comet parameters file
 - Optimize resource allocations
-- Template update 2.9. [#274](https://github.com/nf-core/mhcquant/pull/274)
+- Template update 2.9 [#274](https://github.com/nf-core/mhcquant/pull/274)
+- Improved quantification such that merged FDR-filtered runs can be quantified properly
+- Template update 2.10 [#282](https://github.com/nf-core/mhcquant/pull/282)
 
 ### `Fixed`
 
-- [#266](https://github.com/nf-core/mhcquant/pull/266) New OpenMS version 2.9.1 fixes duplicated ID bug [#250](https://github.com/nf-core/mhcquant/issues/250)
+- [#266](https://github.com/nf-core/mhcquant/pull/266) New OpenMS version 3.0.0 fixes duplicated ID bug [#250](https://github.com/nf-core/mhcquant/issues/250)
 
 ### `Dependencies`
 
-- [#266](https://github.com/nf-core/mhcquant/pull/266) Switched from OpenMS version 2.8.0 to newest version 2.9.1 [#265](https://github.com/nf-core/mhcquant/issues/265)
+- [#266](https://github.com/nf-core/mhcquant/pull/266) Switched from OpenMS version 2.8.0 to newest version 3.0.0 [#265](https://github.com/nf-core/mhcquant/issues/265)
 - [#266](https://github.com/nf-core/mhcquant/pull/266) Bumped ThermoRawFileParser version from 1.4.0 to 1.4.2
 
 ### `Deprecated`
 
+- OpenMS RT prediction
+
 ## v2.4.1 nfcore/mhcquant "Young Shark" (patch) - 2023/04/04
 
 ### `Added`