Merge pull request #625 from bigbio/dev

Release 1.7.0 - Major changes with quantms-rescoring

Author: ypriverol

.devcontainer/setup.sh

@@ -0,0 +1,13 @@
+#!/usr/bin/env bash
+
+# Customise the terminal command prompt
+echo "export PROMPT_DIRTRIM=2" >> $HOME/.bashrc
+echo "export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '" >> $HOME/.bashrc
+export PROMPT_DIRTRIM=2
+export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
+
+# Update Nextflow
+nextflow self-update
+
+# Update welcome message
+echo "Welcome to the bigbio/quantms devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt

.editorconfig

@@ -25,9 +25,9 @@ runs:
         version: "${{ env.NXF_VERSION }}"
 
     - name: Set up Python
-      uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
       with:
-        python-version: "3.13"
+        python-version: "3.14"
 
     - name: Install nf-test
       uses: nf-core/setup-nf-test@v1
@@ -52,6 +52,8 @@ runs:
       with:
         auto-update-conda: true
         conda-solver: libmamba
+        channels: conda-forge
+        channel-priority: strict
         conda-remove-defaults: true
 
     - name: Run nf-test

.github/actions/nf-test/action.yml

@@ -34,8 +34,17 @@ jobs:
       fail-fast: false
       matrix:
         NXF_VER:
-          - "24.10.5"
-        test_profile: ["test_lfq", "test_dia", "test_localize", "test_tmt", "test_dda_id"]
+          - "25.04.0"
+        test_profile:
+          [
+            "test_lfq",
+            "test_dia",
+            "test_localize",
+            "test_tmt",
+            "test_dda_id_alphapeptdeep",
+            "test_dda_id_ms2pip",
+            "test_dda_id_fine_tuning",
+          ]
         exec_profile: ["docker"] # extended ci tests singularity.
 
     steps:

.github/workflows/ci.yml

@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@5bef64f19d7facfb25b37b414482c7164d639639 # v9
+      - uses: actions/stale@5f858e3efba33a5ca4407a664cc011ad407f2008 # v10
         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."

.github/workflows/clean-up.yml

@@ -38,7 +38,7 @@ jobs:
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
         with:
-          version: "24.10.5" # Or the Nextflow version you prefer
+          version: "25.04.0" # Or the Nextflow version you prefer
 
       - name: Log in to GitHub Container Registry
         uses: docker/login-action@v3

.github/workflows/diann_private.yml

@@ -28,25 +28,34 @@ jobs:
       fail-fast: false
       matrix:
         NXF_VER:
-          - "24.10.5"
+          - "25.04.0"
           - "latest-everything"
-        test_profile: ["test_lfq", "test_dia", "test_localize", "test_tmt", "test_dda_id", "test_tmt_corr"]
+        test_profile:
+          [
+            "test_lfq",
+            "test_dia",
+            "test_localize",
+            "test_tmt",
+            "test_dda_id_alphapeptdeep",
+            "test_dda_id_fine_tuning",
+            "test_dda_id_ms2pip",
+            "test_tmt_corr",
+          ]
     env:
       NXF_ANSI_LOG: false
       CAPSULE_LOG: none
       TEST_PROFILE: ${{ matrix.test_profile }}
       EXEC_PROFILE: docker
+
     steps:
-      - name: Check out pipeline code
+      - name: Checkout repository
         uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
 
-      - uses: actions/setup-java@v4
+      - name: Set up Java 17
+        uses: actions/setup-java@v4
         with:
           distribution: "temurin"
           java-version: "17"
-
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
         with:
@@ -111,9 +120,19 @@ jobs:
       fail-fast: false
       matrix:
         NXF_VER:
-          - "24.10.5"
+          - "25.04.0"
           - "latest-everything"
-        test_profile: ["test_lfq", "test_dia", "test_localize", "test_tmt", "test_dda_id", "test_tmt_corr"]
+        test_profile:
+          [
+            "test_lfq",
+            "test_dia",
+            "test_localize",
+            "test_tmt",
+            "test_dda_id_ms2pip",
+            "test_dda_id_alphapeptdeep",
+            "test_tmt_corr",
+            "test_dda_id_fine_tuning",
+          ]
     env:
       NXF_ANSI_LOG: false
       CAPSULE_LOG: none

.github/workflows/extended_ci.yml

@@ -13,13 +13,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
       # indication that the linting is being fixed
       - name: React on comment
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: eyes
@@ -32,9 +32,9 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -47,7 +47,7 @@ jobs:
       # indication that the linting has finished
       - name: react if linting finished succesfully
         if: steps.pre-commit.outcome == 'success'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: "+1"
@@ -67,21 +67,21 @@ jobs:
       - name: react if linting errors were fixed
         id: react-if-fixed
         if: steps.commit-and-push.outcome == 'success'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: hooray
 
       - name: react if linting errors were not fixed
         if: steps.commit-and-push.outcome == 'failure'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: confused
 
       - name: react if linting errors were not fixed
         if: steps.commit-and-push.outcome  == 'failure'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           issue-number: ${{ github.event.issue.number }}
           body: |

.github/workflows/fix_linting.yml

@@ -11,12 +11,12 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
-      - name: Set up Python 3.13
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - name: Set up Python 3.14
+        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -28,14 +28,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
           architecture: "x64"
 
       - name: read .nf-core.yml
@@ -71,7 +71,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: linting-logs
           path: |

.github/workflows/linting.yml

@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@52423e01640425a022ef5fd42c6fb5f633a02728 # v2
+        uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}