Skip to content

Commit 1f25a71

Browse files
nf-core-botnf-core-bot
committed
Template update for nf-core/tools version 2.12
1 parent 1b14283 commit 1f25a71

36 files changed

+490
-221
lines changed

‎.editorconfig

+8
Original file line numberDiff line numberDiff line change
@@ -22,3 +22,11 @@ indent_size = unset
2222

2323
[/assets/email*]
2424
indent_size = unset
25+
26+
# ignore Readme
27+
[README.md]
28+
indent_style = unset
29+
30+
# ignore python
31+
[*.{py}]
32+
indent_style = unset

‎.github/workflows/awsfulltest.yml

+1-1
Original file line numberDiff line numberDiff line change
@@ -31,7 +31,7 @@ jobs:
3131
}
3232
profiles: test_full
3333

34-
- uses: actions/upload-artifact@v3
34+
- uses: actions/upload-artifact@v4
3535
with:
3636
name: Tower debug log file
3737
path: |

‎.github/workflows/awstest.yml

+1-1
Original file line numberDiff line numberDiff line change
@@ -25,7 +25,7 @@ jobs:
2525
}
2626
profiles: test
2727

28-
- uses: actions/upload-artifact@v3
28+
- uses: actions/upload-artifact@v4
2929
with:
3030
name: Tower debug log file
3131
path: |

‎.github/workflows/branch.yml

+1-1
Original file line numberDiff line numberDiff line change
@@ -19,7 +19,7 @@ jobs:
1919
# NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
2020
- name: Post PR comment
2121
if: failure()
22-
uses: mshick/add-pr-comment@v1
22+
uses: mshick/add-pr-comment@v2
2323
with:
2424
message: |
2525
## This PR is against the `master` branch :x:

‎.github/workflows/clean-up.yml

+1-1
Original file line numberDiff line numberDiff line change
@@ -10,7 +10,7 @@ jobs:
1010
issues: write
1111
pull-requests: write
1212
steps:
13-
- uses: actions/stale@v7
13+
- uses: actions/stale@v9
1414
with:
1515
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."
1616
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/download_pipeline.yml

+67
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,67 @@
1+
name: Test successful pipeline download with 'nf-core download'
2+
3+
# Run the workflow when:
4+
# - dispatched manually
5+
# - when a PR is opened or reopened to master branch
6+
# - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev.
7+
on:
8+
workflow_dispatch:
9+
pull_request:
10+
types:
11+
- opened
12+
branches:
13+
- master
14+
pull_request_target:
15+
branches:
16+
- master
17+
18+
env:
19+
NXF_ANSI_LOG: false
20+
21+
jobs:
22+
download:
23+
runs-on: ubuntu-latest
24+
steps:
25+
- name: Install Nextflow
26+
uses: nf-core/setup-nextflow@v1
27+
28+
- uses: actions/setup-python@v5
29+
with:
30+
python-version: "3.11"
31+
architecture: "x64"
32+
- uses: eWaterCycle/setup-singularity@v7
33+
with:
34+
singularity-version: 3.8.3
35+
36+
- name: Install dependencies
37+
run: |
38+
python -m pip install --upgrade pip
39+
pip install git+https://github.com/nf-core/tools.git@dev
40+
41+
- name: Get the repository name and current branch set as environment variable
42+
run: |
43+
echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV}
44+
echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
45+
echo "REPO_BRANCH=${GITHUB_REF#refs/heads/}" >> ${GITHUB_ENV}
46+
47+
- name: Download the pipeline
48+
env:
49+
NXF_SINGULARITY_CACHEDIR: ./
50+
run: |
51+
nf-core download ${{ env.REPO_LOWERCASE }} \
52+
--revision ${{ env.REPO_BRANCH }} \
53+
--outdir ./${{ env.REPOTITLE_LOWERCASE }} \
54+
--compress "none" \
55+
--container-system 'singularity' \
56+
--container-library "quay.io" -l "docker.io" -l "ghcr.io" \
57+
--container-cache-utilisation 'amend' \
58+
--download-configuration
59+
60+
- name: Inspect download
61+
run: tree ./${{ env.REPOTITLE_LOWERCASE }}
62+
63+
- name: Run the downloaded pipeline
64+
env:
65+
NXF_SINGULARITY_CACHEDIR: ./
66+
NXF_SINGULARITY_HOME_MOUNT: true
67+
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results

‎.github/workflows/fix-linting.yml

+53-19
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@ on:
44
types: [created]
55

66
jobs:
7-
deploy:
7+
fix-linting:
88
# Only run if comment is on a PR with the main repo, and if it contains the magic keywords
99
if: >
1010
contains(github.event.comment.html_url, '/pull/') &&
@@ -13,43 +13,77 @@ jobs:
1313
runs-on: ubuntu-latest
1414
steps:
1515
# Use the @nf-core-bot token to check out so we can push later
16-
- uses: actions/checkout@v4
16+
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
1717
with:
1818
token: ${{ secrets.nf_core_bot_auth_token }}
1919

20+
# indication that the linting is being fixed
21+
- name: React on comment
22+
uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
23+
with:
24+
comment-id: ${{ github.event.comment.id }}
25+
reactions: eyes
26+
2027
# Action runs on the issue comment, so we don't get the PR by default
2128
# Use the gh cli to check out the PR
2229
- name: Checkout Pull Request
2330
run: gh pr checkout ${{ github.event.issue.number }}
2431
env:
2532
GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
2633

27-
- uses: actions/setup-node@v4
34+
# Install and run pre-commit
35+
- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
36+
with:
37+
python-version: 3.11
2838

29-
- name: Install Prettier
30-
run: npm install -g prettier @prettier/plugin-php
39+
- name: Install pre-commit
40+
run: pip install pre-commit
3141

32-
# Check that we actually need to fix something
33-
- name: Run 'prettier --check'
34-
id: prettier_status
35-
run: |
36-
if prettier --check ${GITHUB_WORKSPACE}; then
37-
echo "result=pass" >> $GITHUB_OUTPUT
38-
else
39-
echo "result=fail" >> $GITHUB_OUTPUT
40-
fi
42+
- name: Run pre-commit
43+
id: pre-commit
44+
run: pre-commit run --all-files
45+
continue-on-error: true
4146

42-
- name: Run 'prettier --write'
43-
if: steps.prettier_status.outputs.result == 'fail'
44-
run: prettier --write ${GITHUB_WORKSPACE}
47+
# indication that the linting has finished
48+
- name: react if linting finished succesfully
49+
if: steps.pre-commit.outcome == 'success'
50+
uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
51+
with:
52+
comment-id: ${{ github.event.comment.id }}
53+
reactions: "+1"
4554

4655
- name: Commit & push changes
47-
if: steps.prettier_status.outputs.result == 'fail'
56+
id: commit-and-push
57+
if: steps.pre-commit.outcome == 'failure'
4858
run: |
4959
git config user.email "[email protected]"
5060
git config user.name "nf-core-bot"
5161
git config push.default upstream
5262
git add .
5363
git status
54-
git commit -m "[automated] Fix linting with Prettier"
64+
git commit -m "[automated] Fix code linting"
5565
git push
66+
67+
- name: react if linting errors were fixed
68+
id: react-if-fixed
69+
if: steps.commit-and-push.outcome == 'success'
70+
uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
71+
with:
72+
comment-id: ${{ github.event.comment.id }}
73+
reactions: hooray
74+
75+
- name: react if linting errors were not fixed
76+
if: steps.commit-and-push.outcome == 'failure'
77+
uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
78+
with:
79+
comment-id: ${{ github.event.comment.id }}
80+
reactions: confused
81+
82+
- name: react if linting errors were not fixed
83+
if: steps.commit-and-push.outcome == 'failure'
84+
uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
85+
with:
86+
issue-number: ${{ github.event.issue.number }}
87+
body: |
88+
@${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually.
89+
See [CI log](https://github.com/nf-core/rnavar/actions/runs/${{ github.run_id }}) for more details.

‎.github/workflows/linting.yml

+11-50
Original file line numberDiff line numberDiff line change
@@ -11,61 +11,22 @@ on:
1111
types: [published]
1212

1313
jobs:
14-
EditorConfig:
14+
pre-commit:
1515
runs-on: ubuntu-latest
1616
steps:
1717
- uses: actions/checkout@v4
1818

19-
- uses: actions/setup-node@v4
20-
21-
- name: Install editorconfig-checker
22-
run: npm install -g editorconfig-checker
23-
24-
- name: Run ECLint check
25-
run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
26-
27-
Prettier:
28-
runs-on: ubuntu-latest
29-
steps:
30-
- uses: actions/checkout@v4
31-
32-
- uses: actions/setup-node@v4
33-
34-
- name: Install Prettier
35-
run: npm install -g prettier
36-
37-
- name: Run Prettier --check
38-
run: prettier --check ${GITHUB_WORKSPACE}
39-
40-
PythonBlack:
41-
runs-on: ubuntu-latest
42-
steps:
43-
- uses: actions/checkout@v4
44-
45-
- name: Check code lints with Black
46-
uses: psf/black@stable
47-
48-
# If the above check failed, post a comment on the PR explaining the failure
49-
- name: Post PR comment
50-
if: failure()
51-
uses: mshick/add-pr-comment@v1
19+
- name: Set up Python 3.11
20+
uses: actions/setup-python@v5
5221
with:
53-
message: |
54-
## Python linting (`black`) is failing
55-
56-
To keep the code consistent with lots of contributors, we run automated code consistency checks.
57-
To fix this CI test, please run:
58-
59-
* Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
60-
* Fix formatting errors in your pipeline: `black .`
61-
62-
Once you push these changes the test should pass, and you can hide this comment :+1:
22+
python-version: 3.11
23+
cache: "pip"
6324

64-
We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
25+
- name: Install pre-commit
26+
run: pip install pre-commit
6527

66-
Thanks again for your contribution!
67-
repo-token: ${{ secrets.GITHUB_TOKEN }}
68-
allow-repeats: false
28+
- name: Run pre-commit
29+
run: pre-commit run --all-files
6930

7031
nf-core:
7132
runs-on: ubuntu-latest
@@ -76,7 +37,7 @@ jobs:
7637
- name: Install Nextflow
7738
uses: nf-core/setup-nextflow@v1
7839

79-
- uses: actions/setup-python@v4
40+
- uses: actions/setup-python@v5
8041
with:
8142
python-version: "3.11"
8243
architecture: "x64"
@@ -99,7 +60,7 @@ jobs:
9960

10061
- name: Upload linting log file artifact
10162
if: ${{ always() }}
102-
uses: actions/upload-artifact@v3
63+
uses: actions/upload-artifact@v4
10364
with:
10465
name: linting-logs
10566
path: |

‎.github/workflows/linting_comment.yml

+1-1
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@ jobs:
1111
runs-on: ubuntu-latest
1212
steps:
1313
- name: Download lint results
14-
uses: dawidd6/action-download-artifact@v2
14+
uses: dawidd6/action-download-artifact@v3
1515
with:
1616
workflow: linting.yml
1717
workflow_conclusion: completed

‎.github/workflows/release-announcements.yml

+2-2
Original file line numberDiff line numberDiff line change
@@ -24,7 +24,7 @@ jobs:
2424
runs-on: ubuntu-latest
2525

2626
steps:
27-
- uses: actions/setup-python@v4
27+
- uses: actions/setup-python@v5
2828
with:
2929
python-version: "3.10"
3030
- name: Install dependencies
@@ -56,7 +56,7 @@ jobs:
5656
bsky-post:
5757
runs-on: ubuntu-latest
5858
steps:
59-
- uses: zentered/bluesky-post-action@v0.0.2
59+
- uses: zentered/bluesky-post-action@v0.1.0
6060
with:
6161
post: |
6262
Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!

‎.gitpod.yml

+1
Original file line numberDiff line numberDiff line change
@@ -7,6 +7,7 @@ tasks:
77
- name: unset JAVA_TOOL_OPTIONS
88
command: |
99
unset JAVA_TOOL_OPTIONS
10+
1011
vscode:
1112
extensions: # based on nf-core.nf-core-extensionpack
1213
- codezombiech.gitignore # Language support for .gitignore files

‎.pre-commit-config.yaml

+6-1
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,10 @@
11
repos:
22
- repo: https://github.com/pre-commit/mirrors-prettier
3-
rev: "v2.7.1"
3+
rev: "v3.1.0"
44
hooks:
55
- id: prettier
6+
- repo: https://github.com/editorconfig-checker/editorconfig-checker.python
7+
rev: "2.7.3"
8+
hooks:
9+
- id: editorconfig-checker
10+
alias: ec

‎README.md

+6-2
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,9 @@
1-
# ![nf-core/rnavar](docs/images/nf-core-rnavar_logo_light.png#gh-light-mode-only) ![nf-core/rnavar](docs/images/nf-core-rnavar_logo_dark.png#gh-dark-mode-only)
2-
1+
<h1>
2+
<picture>
3+
<source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-rnavar_logo_dark.png">
4+
<img alt="nf-core/rnavar" src="docs/images/nf-core-rnavar_logo_light.png">
5+
</picture>
6+
</h1>
37
[![GitHub Actions CI Status](https://github.com/nf-core/rnavar/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/rnavar/actions?query=workflow%3A%22nf-core+CI%22)
48
[![GitHub Actions Linting Status](https://github.com/nf-core/rnavar/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/rnavar/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnavar/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
59

‎assets/email_template.html

+1-1
Original file line numberDiff line numberDiff line change
@@ -12,7 +12,7 @@
1212

1313
<img src="cid:nfcorepipelinelogo">
1414

15-
<h1>nf-core/rnavar v${version}</h1>
15+
<h1>nf-core/rnavar ${version}</h1>
1616
<h2>Run Name: $runName</h2>
1717

1818
<% if (!success){

‎assets/email_template.txt

+1-1
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@
44
|\\ | |__ __ / ` / \\ |__) |__ } {
55
| \\| | \\__, \\__/ | \\ |___ \\`-._,-`-,
66
`._,._,'
7-
nf-core/rnavar v${version}
7+
nf-core/rnavar ${version}
88
----------------------------------------------------
99
Run Name: $runName
1010

‎assets/nf-core-rnavar_logo_light.png

2.98 KB
Loading

‎docs/images/nf-core-rnavar_logo_dark.png

-38.9 KB
Loading

‎docs/images/nf-core-rnavar_logo_light.png

-42.1 KB
Loading

0 commit comments

Comments
 (0)