Merge pull request #316 from nf-core/dev

Release PR for 1.1.4

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

.github/workflows/ci.yml

@@ -70,33 +70,33 @@ jobs:
 
       - name: Run pipeline with test data (BGC workflow)
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_bgc,docker --outdir ./results ${{ matrix.parameters }}
+          nextflow run ${GITHUB_WORKSPACE} -profile test_bgc,docker --outdir ./results ${{ matrix.parameters }} --bgc_skip_deepbgc
 
-  # test_deeparg: #Tests switched off as long as DeepARG servers are unavaiable for database download.
-  #   name: Run pipeline with test data (DeepARG only workflow)
-  #   # Only run on push if this is the nf-core dev branch (merged PRs)
-  #   if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/funcscan') }}"
-  #   runs-on: ubuntu-latest
-  #   strategy:
-  #     matrix:
-  #       NXF_VER:
-  #         - "23.04.0"
-  #         - "latest-everything"
-  #       parameters:
-  #         - "--annotation_tool bakta --annotation_bakta_db_downloadtype light"
-  #         - "--annotation_tool prodigal"
-  #         - "--annotation_tool prokka"
-  #         - "--annotation_tool pyrodigal"
+  test_deeparg:
+    name: Run pipeline with test data (DeepARG only workflow)
+    # Only run on push if this is the nf-core dev branch (merged PRs)
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/funcscan') }}"
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        NXF_VER:
+          - "23.04.0"
+          - "latest-everything"
+        parameters:
+          - "--annotation_tool bakta --annotation_bakta_db_downloadtype light"
+          - "--annotation_tool pyrodigal"
 
-  #   steps:
-  #     - name: Check out pipeline code
-  #       uses: actions/checkout@v2
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
 
-  #     - name: Install Nextflow
-  #       uses: nf-core/setup-nextflow@v1
-  #       with:
-  #         version: "${{ matrix.NXF_VER }}"
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "${{ matrix.NXF_VER }}"
 
-  #     - name: Run pipeline with test data (DeepARG workflow)
-  #       run: |
-  #         nextflow run ${GITHUB_WORKSPACE} -profile test_deeparg,docker --outdir ./results ${{ matrix.parameters }}
+      - name: Run pipeline with test data (DeepARG workflow)
+        run: |
+          wget https://zenodo.org/record/8280582/files/deeparg.zip ## download from zenodo due to instability of deepARG server
+          unzip deeparg.zip
+          nextflow run ${GITHUB_WORKSPACE} -profile test_deeparg,docker --outdir ./results ${{ matrix.parameters }} --arg_deeparg_data 'deeparg/'

.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 }}
+          #

CHANGELOG.md

@@ -3,6 +3,29 @@
 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).
 
+## v1.1.4 - [2023-11-07]
+
+### `Added`
+
+### `Fixed`
+
+- [#306](https://github.com/nf-core/funcscan/pull/306) Added new parameter `annotation_prokka_retaincontigheaders` to allow prokka to retain the original contig headers/locus tag. (by @darcy220606)
+- [#307](https://github.com/nf-core/funcscan/pull/307) Fixed stability of deepARG tests by using Zenodo copy of database (❤️ to Gustavo Arango and Liqing Zhang for uploading, fix by @jfy133)
+- [#310](https://github.com/nf-core/funcscan/pull/310) Fixed error when supplying uncompressed input; added "fas" file extension for FASTA files. (by @tavareshugo)
+- [#311](https://github.com/nf-core/funcscan/pull/311) Merged pipeline template of nf-core/tools version 2.10. (by @jasmezz)
+
+### `Dependencies`
+
+| Tool          | Previous version | New version |
+| ------------- | ---------------- | ----------- |
+| AMRFinderPlus | 3.10.42          | 3.11.18     |
+| Bakta         | 1.7.0            | 1.8.2       |
+| MultiQC       | 1.14            | 1.15       |
+
+### `Deprecated`
+
+- FastQC
+
 ## v1.1.3 - [2023-08-11]
 
 ### `Added`