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Merge pull request #87 from sanger-tol/dev
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Release 0.2.0 - no review done
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priyanka-surana authored Dec 22, 2023
2 parents 7f201b4 + bc9fa62 commit 735b30d
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1 change: 1 addition & 0 deletions .devcontainer/devcontainer.json
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Expand Up @@ -2,6 +2,7 @@
"name": "nfcore",
"image": "nfcore/gitpod:latest",
"remoteUser": "gitpod",
"runArgs": ["--privileged"],

// Configure tool-specific properties.
"customizations": {
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9 changes: 9 additions & 0 deletions .editorconfig
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Expand Up @@ -31,3 +31,12 @@ insert_final_newline = unset
trim_trailing_whitespace = unset
indent_style = unset
indent_size = unset

# To prevent errors for these test blastn databases
[/assets/test*/nt_*/*.{ndb,nhr,nin,nog,nos,not,nsq,ntf,nto}]
charset = unset
end_of_line = unset
insert_final_newline = unset
trim_trailing_whitespace = unset
indent_style = unset
indent_size = unset
4 changes: 3 additions & 1 deletion .github/CONTRIBUTING.md
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Expand Up @@ -23,6 +23,9 @@ If you're not used to this workflow with git, you can start with some [docs from

## Tests

You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to
receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir <OUTDIR>`.

When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.

Expand Down Expand Up @@ -110,4 +113,3 @@ To get started:
Devcontainer specs:

- [DevContainer config](.devcontainer/devcontainer.json)
- [Dockerfile](.devcontainer/Dockerfile)
40 changes: 18 additions & 22 deletions .github/ISSUE_TEMPLATE/bug_report.yml
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Expand Up @@ -2,53 +2,49 @@ name: Bug report
description: Report something that is broken or incorrect
labels: bug
body:
- type: markdown
attributes:
value: |
Before you post this issue, please check the documentation:
- [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
- [sanger-tol/blobtoolkit pipeline documentation](https://pipelines.tol.sanger.ac.uk/blobtoolkit/usage)
- type: textarea
id: description
attributes:
label: Description of the bug
description: A clear and concise description of what the bug is.
validations:
required: true

- type: textarea
id: command_used
attributes:
label: Command used and terminal output
description: Steps to reproduce the behaviour. Please paste the command you used
to launch the pipeline and the output from your terminal.
description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
render: console
placeholder: "$ nextflow run ...
placeholder: |
$ nextflow run ...
Some output where something broke
"
- type: textarea
id: files
attributes:
label: Relevant files
description: "Please drag and drop the relevant files here. Create a `.zip` archive
if the extension is not allowed.
Your verbose log file `.nextflow.log` is often useful _(this is a hidden file
in the directory where you launched the pipeline)_ as well as custom Nextflow
configuration files.
description: |
Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed.
Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.
"
- type: textarea
id: system
attributes:
label: System information
description: "* Nextflow version _(eg. 22.10.1)_
description: |
* Nextflow version _(eg. 23.04.0)_
* Hardware _(eg. HPC, Desktop, Cloud)_
* Executor _(eg. slurm, local, awsbatch)_
* Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud,
or Apptainer)_
* Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
* OS _(eg. CentOS Linux, macOS, Linux Mint)_
* Version of sanger-tol/blobtoolkit _(eg. 1.1, 1.5, 1.8.2)_
"
7 changes: 0 additions & 7 deletions .github/ISSUE_TEMPLATE/config.yml

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5 changes: 3 additions & 2 deletions .github/PULL_REQUEST_TEMPLATE.md
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Expand Up @@ -8,16 +8,17 @@ These are the most common things requested on pull requests (PRs).
Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
Learn more about contributing: [CONTRIBUTING.md](https://github.com/sanger-tol/blobtoolkit/tree/master/.github/CONTRIBUTING.md)
Learn more about contributing: [CONTRIBUTING.md](.github/CONTRIBUTING.md)
-->

## PR checklist

- [ ] This comment contains a description of changes (with reason).
- [ ] If you've fixed a bug or added code that should be tested, add tests!
- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/sanger-tol/blobtoolkit/tree/master/.github/CONTRIBUTING.md)
- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](.github/CONTRIBUTING.md)
- [ ] Make sure your code lints (`nf-core lint`).
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
- [ ] Usage Documentation in `docs/usage.md` is updated.
- [ ] Output Documentation in `docs/output.md` is updated.
- [ ] `CHANGELOG.md` is updated.
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23 changes: 19 additions & 4 deletions .github/workflows/ci.yml
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@@ -1,7 +1,12 @@
name: nf-core CI
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
on:
workflow_dispatch:
push:
branches:
- dev
pull_request:
release:
types: [published]

env:
NXF_ANSI_LOG: false
Expand All @@ -19,20 +24,30 @@ jobs:
strategy:
matrix:
NXF_VER:
- "22.10.1"
- "23.04.0"
- "latest-everything"
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
uses: actions/checkout@v4

- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"

- name: Download the NCBI taxdump database
run: |
mkdir ncbi_taxdump
curl -L https://ftp.ncbi.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz | tar -C ncbi_taxdump -xzf -
- name: Download the BUSCO lineage database
run: |
mkdir busco_database
curl -L https://tolit.cog.sanger.ac.uk/test-data/resources/busco/blobtoolkit.GCA_922984935.2.2023-08-03.lineages.tar.gz | tar -C busco_database -xzf -
- name: Run pipeline with test data
# You can customise CI pipeline run tests as required
# For example: adding multiple test runs with different parameters
# Remember that you can parallelise this by using strategy.matrix
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --taxdump $PWD/ncbi_taxdump --busco $PWD/busco_database --outdir ./results
16 changes: 8 additions & 8 deletions .github/workflows/fix-linting.yml
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Expand Up @@ -8,23 +8,23 @@ jobs:
# Only run if comment is on a PR with the main repo, and if it contains the magic keywords
if: >
contains(github.event.comment.html_url, '/pull/') &&
contains(github.event.comment.body, '@nf-core-bot fix linting') &&
contains(github.event.comment.body, '@sanger-tolsoft fix linting') &&
github.repository == 'sanger-tol/blobtoolkit'
runs-on: ubuntu-latest
steps:
# Use the @nf-core-bot token to check out so we can push later
- uses: actions/checkout@v3
# Use the @sanger-tolsoft token to check out so we can push later
- uses: actions/checkout@v4
with:
token: ${{ secrets.nf_core_bot_auth_token }}
token: ${{ secrets.sangertolsoft_access_token }}

# Action runs on the issue comment, so we don't get the PR by default
# Use the gh cli to check out the PR
- name: Checkout Pull Request
run: gh pr checkout ${{ github.event.issue.number }}
env:
GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
GITHUB_TOKEN: ${{ secrets.sangertolsoft_access_token }}

- uses: actions/setup-node@v3
- uses: actions/setup-node@v4

- name: Install Prettier
run: npm install -g prettier @prettier/plugin-php
Expand All @@ -46,8 +46,8 @@ jobs:
- name: Commit & push changes
if: steps.prettier_status.outputs.result == 'fail'
run: |
git config user.email "[email protected]"
git config user.name "nf-core-bot"
git config user.email "[email protected]"
git config user.name "sanger-tolsoft"
git config push.default upstream
git add .
git status
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14 changes: 7 additions & 7 deletions .github/workflows/linting.yml
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Expand Up @@ -14,9 +14,9 @@ jobs:
EditorConfig:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- uses: actions/setup-node@v3
- uses: actions/setup-node@v4

- name: Install editorconfig-checker
run: npm install -g editorconfig-checker
Expand All @@ -27,9 +27,9 @@ jobs:
Prettier:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- uses: actions/setup-node@v3
- uses: actions/setup-node@v4

- name: Install Prettier
run: npm install -g prettier
Expand All @@ -40,7 +40,7 @@ jobs:
PythonBlack:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- name: Check code lints with Black
uses: psf/black@stable
Expand Down Expand Up @@ -71,14 +71,14 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
uses: actions/checkout@v4

- name: Install Nextflow
uses: nf-core/setup-nextflow@v1

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

- name: Install dependencies
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68 changes: 68 additions & 0 deletions .github/workflows/release-announcements.yml
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@@ -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 }}
#
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@@ -1,4 +1,4 @@
name: nf-core Sanger LSF tests
name: sanger-tol LSF tests

on:
workflow_dispatch:
Expand All @@ -13,16 +13,21 @@ jobs:
if: github.event_name == 'workflow_dispatch'

- name: Launch workflow via tower
uses: nf-core/tower-action@v2
uses: seqeralabs/action-tower-launch@v2
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
pipeline: ${{ github.repository }}
revision: ${{ env.REVISION }}
workdir: ${{ secrets.TOWER_WORKDIR_PARENT }}/work/${{ github.repository }}/work-${{ env.REVISION }}
parameters: |
{
"outdir": "${{ secrets.TOWER_WORKDIR_PARENT }}/results/${{ github.repository }}/results-${{ env.REVISION }}",
}
profiles: test,sanger,singularity,cleanup
- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: |
tower_action_*.log
tower_action_*.json
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