Merge branch 'main' into rich-codex-token

nf-core · May 21, 2024 · 7b9da9d · 7b9da9d
2 parents ec5f8f2 + 872666d
commit 7b9da9d
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Showing 10 changed files with 135 additions and 74 deletions.
diff --git a/.cache.tar.xz b/.cache.tar.xz
diff --git a/.github/workflows/add-netlify-link.yml b/.github/workflows/add-netlify-link.yml
@@ -12,7 +12,7 @@ jobs:
     steps:
       - name: Check for changed files
         id: changed-files
-        uses: tj-actions/changed-files@0874344d6ebbaa00a27da73276ae7162fadcaf69 # v44
+        uses: tj-actions/changed-files@a29e8b565651ce417abb5db7164b4a2ad8b6155c # v44
 
       - name: Add Netlify link to PR
         if: steps.changed-files.outputs.all_changed_files != ''

diff --git a/.github/workflows/build-json-files-and-md-cache.yml b/.github/workflows/build-json-files-and-md-cache.yml
@@ -18,7 +18,7 @@ jobs:
         id: date
         run: echo "::set-output name=date::$(date +'%Y-%m-%d')"
       # Set up the main website repo
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
         with:
           fetch-depth: 0 # Don't do a shallow clone
           token: ${{secrets.NF_CORE_BOT_AUTH_TOKEN}} # Needed for pushing back to the repo

diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -9,7 +9,7 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
       - uses: actions/setup-node@60edb5dd545a775178f52524783378180af0d1f8 # v4
         with:
           node-version: 20
@@ -18,7 +18,7 @@ jobs:
   vale:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
       - name: Install Vale
         run: |
           wget https://github.com/errata-ai/vale/releases/download/v3.0.5/vale_3.0.5_Linux_64-bit.tar.gz -O vale.tar.gz

diff --git a/.github/workflows/playwright.yml b/.github/workflows/playwright.yml
@@ -12,7 +12,7 @@ jobs:
     timeout-minutes: 30
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
       - uses: actions/setup-node@60edb5dd545a775178f52524783378180af0d1f8 # v4
         with:
           node-version: 18

diff --git a/.github/workflows/rich-codex.yml b/.github/workflows/rich-codex.yml
@@ -6,7 +6,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
         with:
           # Use @nf-core-bot token to check out so we can push without a PR
           token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
@@ -34,3 +34,4 @@ jobs:
           commit_changes: 'true'
           terminal_width: 100
           skip_git_checks: 'true'
+          search_include: '.github/workflows/rich-codex.yml'
diff --git a/public/components.json b/public/components.json
@@ -5422,6 +5422,10 @@
           "name": "rnafusion",
           "version": "3.0.2"
         },
+        {
+          "name": "rnafusion",
+          "version": "3.0.2"
+        },
         {
           "name": "rnafusion",
           "version": "3.0.2"
@@ -17396,6 +17400,10 @@
           "name": "genomeassembler",
           "version": "dev"
         },
+        {
+          "name": "genomeassembler",
+          "version": "dev"
+        },
         {
           "name": "genomeassembler",
           "version": "dev"
@@ -42601,6 +42609,10 @@
           "name": "rnadnavar",
           "version": "dev"
         },
+        {
+          "name": "rnadnavar",
+          "version": "dev"
+        },
         {
           "name": "rnadnavar",
           "version": "dev"
@@ -44758,6 +44770,10 @@
           "name": "rnadnavar",
           "version": "dev"
         },
+        {
+          "name": "rnadnavar",
+          "version": "dev"
+        },
         {
           "name": "rnadnavar",
           "version": "dev"
@@ -50073,6 +50089,10 @@
           "name": "rnadnavar",
           "version": "dev"
         },
+        {
+          "name": "rnadnavar",
+          "version": "dev"
+        },
         {
           "name": "rnadnavar",
           "version": "dev"
@@ -66575,6 +66595,10 @@
           "name": "isoseq",
           "version": "1.1.5"
         },
+        {
+          "name": "isoseq",
+          "version": "1.1.5"
+        },
         {
           "name": "isoseq",
           "version": "1.1.5"
@@ -106309,6 +106333,10 @@
           "name": "callingcards",
           "version": "dev"
         },
+        {
+          "name": "fastquorum",
+          "version": "dev"
+        },
         {
           "name": "hicar",
           "version": "1.0.0"
@@ -127863,7 +127891,13 @@
         "maintainers": [
           "@atrigila"
         ]
-      }
+      },
+      "pipelines": [
+        {
+          "name": "phaseimpute",
+          "version": "dev"
+        }
+      ]
     },
     {
       "name": "vcflib_vcfuniq",