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jasmezzjasmezz
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Merge pull request #316 from nf-core/dev
Release PR for 1.1.4
2 parents eb8f79c + 5c7aebf commit 274042b

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‎.devcontainer/devcontainer.json

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

‎.github/CONTRIBUTING.md

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However, don't be put off by this template - other more general issues and suggestions are welcome!
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Contributions to the code are even more welcome ;)
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> 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)).
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:::info
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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)).
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:::
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## Contribution workflow
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‎.github/workflows/ci.yml

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

‎.github/workflows/linting.yml

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- uses: actions/setup-python@v4
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with:
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python-version: "3.8"
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python-version: "3.11"
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architecture: "x64"
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- name: Install dependencies

‎.github/workflows/release-announcments.yml

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name: release-announcements
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# Automatic release toot and tweet anouncements
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on:
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release:
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types: [published]
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workflow_dispatch:
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jobs:
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toot:
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runs-on: ubuntu-latest
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steps:
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- uses: rzr/fediverse-action@master
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with:
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access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
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host: "mstdn.science" # custom host if not "mastodon.social" (default)
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# GitHub event payload
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# https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release
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message: |
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Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
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Please see the changelog: ${{ github.event.release.html_url }}
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send-tweet:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/setup-python@v4
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with:
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python-version: "3.10"
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- name: Install dependencies
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run: pip install tweepy==4.14.0
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- name: Send tweet
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shell: python
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run: |
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import os
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import tweepy
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client = tweepy.Client(
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access_token=os.getenv("TWITTER_ACCESS_TOKEN"),
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access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"),
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consumer_key=os.getenv("TWITTER_CONSUMER_KEY"),
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consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"),
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)
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tweet = os.getenv("TWEET")
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client.create_tweet(text=tweet)
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env:
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TWEET: |
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Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
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Please see the changelog: ${{ github.event.release.html_url }}
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TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }}
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TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }}
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TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }}
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TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}
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bsky-post:
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runs-on: ubuntu-latest
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steps:
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- uses: zentered/[email protected]
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with:
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post: |
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Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
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Please see the changelog: ${{ github.event.release.html_url }}
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env:
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BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }}
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BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }}
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#

‎CHANGELOG.md

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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## v1.1.4 - [2023-11-07]
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### `Added`
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### `Fixed`
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- [#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)
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- [#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)
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- [#310](https://github.com/nf-core/funcscan/pull/310) Fixed error when supplying uncompressed input; added "fas" file extension for FASTA files. (by @tavareshugo)
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- [#311](https://github.com/nf-core/funcscan/pull/311) Merged pipeline template of nf-core/tools version 2.10. (by @jasmezz)
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### `Dependencies`
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| Tool | Previous version | New version |
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| ------------- | ---------------- | ----------- |
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| AMRFinderPlus | 3.10.42 | 3.11.18 |
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| Bakta | 1.7.0 | 1.8.2 |
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| MultiQC | 1.14 | 1.15 |
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### `Deprecated`
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- FastQC
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## v1.1.3 - [2023-08-11]
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### `Added`

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