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Merge pull request #230 from nf-core/dev
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Release 2.3.0
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jonasscheid authored Feb 26, 2024
2 parents b0f0d7a + 1b82b50 commit e173620
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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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17 changes: 15 additions & 2 deletions .editorconfig
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Expand Up @@ -8,7 +8,7 @@ trim_trailing_whitespace = true
indent_size = 4
indent_style = space

[*.{md,yml,yaml,html,css,scss,js,cff}]
[*.{md,yml,yaml,html,css,scss,js}]
indent_size = 2

# These files are edited and tested upstream in nf-core/modules
Expand All @@ -18,7 +18,20 @@ end_of_line = unset
insert_final_newline = unset
trim_trailing_whitespace = unset
indent_style = unset
indent_size = unset
[/subworkflows/nf-core/**]
charset = unset
end_of_line = unset
insert_final_newline = unset
trim_trailing_whitespace = unset
indent_style = unset

[/assets/email*]
indent_size = unset

# ignore Readme
[README.md]
indent_style = unset

# ignore python
[*.{py,md}]
indent_style = unset
8 changes: 6 additions & 2 deletions .github/CONTRIBUTING.md
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Expand Up @@ -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/epitopeprediction then the best place to ask is on the nf-core Slack [#epitopeprediction](https://nfcore.slack.com/channels/epitopeprediction) channel ([join our Slack here](https://nf-co.re/join/slack)).
:::info
If you need help using or modifying nf-core/epitopeprediction then the best place to ask is on the nf-core Slack [#epitopeprediction](https://nfcore.slack.com/channels/epitopeprediction) channel ([join our Slack here](https://nf-co.re/join/slack)).
:::

## Contribution workflow

Expand All @@ -25,6 +27,9 @@ 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 @@ -116,4 +121,3 @@ To get started:
Devcontainer specs:

- [DevContainer config](.devcontainer/devcontainer.json)
- [Dockerfile](.devcontainer/Dockerfile)
4 changes: 2 additions & 2 deletions .github/ISSUE_TEMPLATE/bug_report.yml
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Expand Up @@ -42,9 +42,9 @@ body:
attributes:
label: System information
description: |
* Nextflow version _(eg. 22.10.1)_
* 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 or Charliecloud)_
* Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
* OS _(eg. CentOS Linux, macOS, Linux Mint)_
* Version of nf-core/epitopeprediction _(eg. 1.1, 1.5, 1.8.2)_
4 changes: 3 additions & 1 deletion .github/PULL_REQUEST_TEMPLATE.md
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Expand Up @@ -15,9 +15,11 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/epit

- [ ] 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/nf-core/epitopeprediction/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/epitopeprediction _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/epitopeprediction/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/epitopeprediction _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
- [ ] 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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13 changes: 9 additions & 4 deletions .github/workflows/awsfulltest.yml
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Expand Up @@ -14,18 +14,23 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Launch workflow via tower
uses: nf-core/tower-action@v3
uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
revision: ${{ github.sha }}
workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/epitopeprediction/work-${{ github.sha }}
parameters: |
{
"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/epitopeprediction/results-${{ github.sha }}"
}
profiles: test_full,aws_tower
- uses: actions/upload-artifact@v3
profiles: test_full

- uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
with:
name: Tower debug log file
path: tower_action_*.log
path: |
tower_action_*.log
tower_action_*.json
12 changes: 8 additions & 4 deletions .github/workflows/awstest.yml
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Expand Up @@ -12,18 +12,22 @@ jobs:
steps:
# Launch workflow using Tower CLI tool action
- name: Launch workflow via tower
uses: nf-core/tower-action@v3
uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
revision: ${{ github.sha }}
workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/epitopeprediction/work-${{ github.sha }}
parameters: |
{
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/epitopeprediction/results-test-${{ github.sha }}"
}
profiles: test,aws_tower
- uses: actions/upload-artifact@v3
profiles: test

- uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
with:
name: Tower debug log file
path: tower_action_*.log
path: |
tower_action_*.log
tower_action_*.json
4 changes: 2 additions & 2 deletions .github/workflows/branch.yml
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Expand Up @@ -13,13 +13,13 @@ jobs:
- name: Check PRs
if: github.repository == 'nf-core/epitopeprediction'
run: |
{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/epitopeprediction ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/epitopeprediction ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
# If the above check failed, post a comment on the PR explaining the failure
# NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
- name: Post PR comment
if: failure()
uses: mshick/add-pr-comment@v1
uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
with:
message: |
## This PR is against the `master` branch :x:
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73 changes: 24 additions & 49 deletions .github/workflows/ci.yml
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Expand Up @@ -24,58 +24,43 @@ 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@b4ffde65f46336ab88eb53be808477a3936bae11 # v4

- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
with:
version: "${{ matrix.NXF_VER }}"

- name: Disk space cleanup
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1

- name: Run pipeline with test data
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
profile:
name: Run profile tests
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/epitopeprediction') }}
runs-on: ubuntu-latest
env:
NXF_VER: ${{ matrix.nxf_ver }}
NXF_ANSI_LOG: false
strategy:
matrix:
include:
# Test pipeline minimum Nextflow version
- NXF_VER: "22.10.1"
NXF_EDGE: ""
# Test latest edge release of Nextflow
- NXF_VER: ""
NXF_EDGE: "1"
NXF_VER:
- "23.04.0"
- "latest-everything"
tests:
[
"test_variant_tsv",
"test_grch38_variant_tsv",
"test_peptides",
"test_peptides_h2",
"test_proteins",
"test_mhcnuggets",
"test_mhcflurry",
]
["test_grch38", "test_peptides", "test_peptides_h2", "test_proteins", "test_mhcnuggets", "test_mhcflurry"]
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
uses: actions/checkout@v3

- name: Install Nextflow
env:
NXF_VER: ${{ matrix.NXF_VER }}
# Uncomment only if the edge release is more recent than the latest stable release
# See https://github.com/nextflow-io/nextflow/issues/2467
# NXF_EDGE: ${{ matrix.NXF_EDGE }}
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"

- name: Run pipeline with profile ${{ matrix.tests }}
run: |
nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.tests }},docker --outdir ./results
Expand All @@ -84,20 +69,14 @@ jobs:
name: Run NetMHC tool family tests
if: ${{ ( github.event_name == 'push' && github.repository == 'nf-core/epitopeprediction' ) || github.event.pull_request.head.repo.full_name == 'nf-core/epitopeprediction' }}
runs-on: ubuntu-latest
env:
NXF_VER: ${{ matrix.nxf_ver }}
strategy:
matrix:
include:
# Test pipeline minimum Nextflow version
- NXF_VER: "22.10.1"
NXF_EDGE: ""
# Test latest edge release of Nextflow
- NXF_VER: ""
NXF_EDGE: "1"
NXF_VER:
- "23.04.0"
- "latest-everything"
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
uses: actions/checkout@v3

- name: Install non-free software
env:
Expand All @@ -107,14 +86,10 @@ jobs:
curl -L https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/software/non-free-software.tar.gpg | ${GITHUB_WORKSPACE}/bin/decrypt | tar -C non-free -v -x
- name: Install Nextflow
env:
NXF_VER: ${{ matrix.NXF_VER }}
# Uncomment only if the edge release is more recent than the latest stable release
# See https://github.com/nextflow-io/nextflow/issues/2467
# NXF_EDGE: ${{ matrix.NXF_EDGE }}
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"

- name: Run pipeline with NetMHC
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_netmhc,docker --outdir ./results
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24 changes: 24 additions & 0 deletions .github/workflows/clean-up.yml
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@@ -0,0 +1,24 @@
name: "Close user-tagged issues and PRs"
on:
schedule:
- cron: "0 0 * * 0" # Once a week

jobs:
clean-up:
runs-on: ubuntu-latest
permissions:
issues: write
pull-requests: write
steps:
- uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9
with:
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."
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."
close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity."
days-before-stale: 30
days-before-close: 20
days-before-pr-close: -1
any-of-labels: "awaiting-changes,awaiting-feedback"
exempt-issue-labels: "WIP"
exempt-pr-labels: "WIP"
repo-token: "${{ secrets.GITHUB_TOKEN }}"
72 changes: 72 additions & 0 deletions .github/workflows/download_pipeline.yml
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@@ -0,0 +1,72 @@
name: Test successful pipeline download with 'nf-core download'

# Run the workflow when:
# - dispatched manually
# - when a PR is opened or reopened to master branch
# - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev.
on:
workflow_dispatch:
inputs:
testbranch:
description: "The specific branch you wish to utilize for the test execution of nf-core download."
required: true
default: "dev"
pull_request:
types:
- opened
branches:
- master
pull_request_target:
branches:
- master

env:
NXF_ANSI_LOG: false

jobs:
download:
runs-on: ubuntu-latest
steps:
- name: Install Nextflow
uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1

- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
with:
python-version: "3.11"
architecture: "x64"
- uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
with:
singularity-version: 3.8.3

- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install git+https://github.com/nf-core/tools.git@dev
- name: Get the repository name and current branch set as environment variable
run: |
echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV}
echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
- name: Download the pipeline
env:
NXF_SINGULARITY_CACHEDIR: ./
run: |
nf-core download ${{ env.REPO_LOWERCASE }} \
--revision ${{ env.REPO_BRANCH }} \
--outdir ./${{ env.REPOTITLE_LOWERCASE }} \
--compress "none" \
--container-system 'singularity' \
--container-library "quay.io" -l "docker.io" -l "ghcr.io" \
--container-cache-utilisation 'amend' \
--download-configuration
- name: Inspect download
run: tree ./${{ env.REPOTITLE_LOWERCASE }}

- name: Run the downloaded pipeline
env:
NXF_SINGULARITY_CACHEDIR: ./
NXF_SINGULARITY_HOME_MOUNT: true
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
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