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Merge pull request #208 from nf-core/dev
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Prepare for release 2.3.0
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marissaDubbelaar authored Apr 5, 2022
2 parents 8447c4d + 61907f4 commit b24db1e
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5 changes: 1 addition & 4 deletions .editorconfig
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Expand Up @@ -8,12 +8,9 @@ trim_trailing_whitespace = true
indent_size = 4
indent_style = space

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

[*.json]
insert_final_newline = unset

# These files are edited and tested upstream in nf-core/modules
[/modules/nf-core/**]
charset = unset
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15 changes: 7 additions & 8 deletions .github/CONTRIBUTING.md
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Expand Up @@ -15,8 +15,7 @@ Contributions to the code are even more welcome ;)

If you'd like to write some code for nf-core/mhcquant, the standard workflow is as follows:

1. Check that there isn't already an issue about your idea in the [nf-core/mhcquant issues](https://github.com/nf-core/mhcquant/issues) to avoid duplicating work
* If there isn't one already, please create one so that others know you're working on this
1. Check that there isn't already an issue about your idea in the [nf-core/mhcquant issues](https://github.com/nf-core/mhcquant/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/mhcquant repository](https://github.com/nf-core/mhcquant) to your GitHub account
3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
Expand Down Expand Up @@ -49,9 +48,9 @@ These tests are run both with the latest available version of `Nextflow` and als

:warning: Only in the unlikely and regretful event of a release happening with a bug.

* On your own fork, make a new branch `patch` based on `upstream/master`.
* Fix the bug, and bump version (X.Y.Z+1).
* A PR should be made on `master` from patch to directly this particular bug.
- On your own fork, make a new branch `patch` based on `upstream/master`.
- Fix the bug, and bump version (X.Y.Z+1).
- A PR should be made on `master` from patch to directly this particular bug.

## Getting help

Expand All @@ -73,7 +72,7 @@ If you wish to contribute a new step, please use the following coding standards:
6. Add sanity checks and validation for all relevant parameters.
7. Perform local tests to validate that the new code works as expected.
8. If applicable, add a new test command in `.github/workflow/ci.yml`.
9. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.

### Default values
Expand All @@ -92,8 +91,8 @@ The process resources can be passed on to the tool dynamically within the proces

Please use the following naming schemes, to make it easy to understand what is going where.

* initial process channel: `ch_output_from_<process>`
* intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`
- initial process channel: `ch_output_from_<process>`
- intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`

### Nextflow version bumping

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2 changes: 0 additions & 2 deletions .github/ISSUE_TEMPLATE/bug_report.yml
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@@ -1,9 +1,7 @@

name: Bug report
description: Report something that is broken or incorrect
labels: bug
body:

- type: markdown
attributes:
value: |
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7 changes: 3 additions & 4 deletions .github/PULL_REQUEST_TEMPLATE.md
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Expand Up @@ -10,16 +10,15 @@ Remember that PRs should be made against the dev branch, unless you're preparing
Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/mhcquant/tree/master/.github/CONTRIBUTING.md)
-->
<!-- markdownlint-disable ul-indent -->

## 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/nf-core/mhcquant/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/mhcquant _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/mhcquant/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/mhcquant _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`).
- [ ] Ensure the test suite passes (`nextflow run . -profile 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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8 changes: 4 additions & 4 deletions .github/workflows/awsfulltest.yml
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Expand Up @@ -14,17 +14,17 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Launch workflow via tower
uses: nf-core/tower-action@v2
uses: nf-core/tower-action@v3
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
pipeline: ${{ github.repository }}
revision: ${{ github.sha }}
workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/mhcquant/work-${{ github.sha }}
parameters: |
{
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/mhcquant/results-${{ github.sha }}"
}
profiles: test_full,aws_tower
pre_run_script: 'export NXF_VER=21.10.3'
nextflow_config: |
process.errorStrategy = 'retry'
process.maxRetries = 3
10 changes: 5 additions & 5 deletions .github/workflows/awstest.yml
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Expand Up @@ -10,19 +10,19 @@ jobs:
if: github.repository == 'nf-core/mhcquant'
runs-on: ubuntu-latest
steps:
# Launch workflow using Tower CLI tool action
- name: Launch workflow via tower
uses: nf-core/tower-action@v2

uses: nf-core/tower-action@v3
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
pipeline: ${{ github.repository }}
revision: ${{ github.sha }}
workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/mhcquant/work-${{ github.sha }}
parameters: |
{
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/mhcquant/results-test-${{ github.sha }}"
}
profiles: test,aws_tower
pre_run_script: 'export NXF_VER=21.10.3'
nextflow_config: |
process.errorStrategy = 'retry'
process.maxRetries = 3
5 changes: 2 additions & 3 deletions .github/workflows/branch.yml
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Expand Up @@ -13,8 +13,7 @@ jobs:
- name: Check PRs
if: github.repository == 'nf-core/mhcquant'
run: |
{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/mhcquant ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
"{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/mhcquant ]] && [[ $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
Expand Down Expand Up @@ -43,4 +42,4 @@ jobs:
Thanks again for your contribution!
repo-token: ${{ secrets.GITHUB_TOKEN }}
allow-repeats: false

#
28 changes: 15 additions & 13 deletions .github/workflows/ci.yml
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Expand Up @@ -14,20 +14,20 @@ env:

jobs:
test:
name: Run workflow tests
name: Run pipeline with test data
# Only run on push if this is the nf-core dev branch (merged PRs)
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mhcquant') }}
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mhcquant') }}"
runs-on: ubuntu-latest
strategy:
matrix:
# Nextflow versions
include:
# Test pipeline minimum Nextflow version
- NXF_VER: '21.10.3'
NXF_EDGE: ''
- NXF_VER: "21.10.3"
NXF_EDGE: ""
# Test latest edge release of Nextflow
- NXF_VER: ''
NXF_EDGE: '1'
- NXF_VER: ""
NXF_EDGE: "1"
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
Expand All @@ -44,23 +44,23 @@ jobs:
- name: Run pipeline with test data
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
test_additional_params:
name: Run pipeline with additional params
# Only run on push if this is the nf-core dev branch (merged PRs)
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mhcquant') }}
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mhcquant') }}"
runs-on: ubuntu-latest
strategy:
matrix:
# Nextflow versions
include:
# Test pipeline minimum Nextflow version
- NXF_VER: '21.10.3'
NXF_EDGE: ''
- NXF_VER: "21.10.3"
NXF_EDGE: ""
# Test latest edge release of Nextflow
- NXF_VER: ''
NXF_EDGE: '1'
- NXF_VER: ""
NXF_EDGE: "1"
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
Expand All @@ -77,4 +77,6 @@ jobs:
- name: Run pipeline with additional params
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --predict_class_1 --predict_class_2 --predict_RT
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --predict_class_1 --predict_class_2 --predict_RT --outdir ./results
#
91 changes: 14 additions & 77 deletions .github/workflows/linting.yml
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@@ -1,107 +1,43 @@
name: nf-core linting
# This workflow is triggered on pushes and PRs to the repository.
# It runs the `nf-core lint` and markdown lint tests to ensure that the code meets the nf-core guidelines
# It runs the `nf-core lint` and markdown lint tests to ensure
# that the code meets the nf-core guidelines.
on:
push:
pull_request:
release:
types: [published]

jobs:
Markdown:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/setup-node@v1
with:
node-version: '10'
- name: Install markdownlint
run: npm install -g markdownlint-cli
- name: Run Markdownlint
run: markdownlint .

# If the above check failed, post a comment on the PR explaining the failure
- name: Post PR comment
if: failure()
uses: mshick/add-pr-comment@v1
with:
message: |
## Markdown linting is failing
To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:
* Install `markdownlint-cli`
* On Mac: `brew install markdownlint-cli`
* Everything else: [Install `npm`](https://www.npmjs.com/get-npm) then [install `markdownlint-cli`](https://www.npmjs.com/package/markdownlint-cli) (`npm install -g markdownlint-cli`)
* Fix the markdown errors
* Automatically: `markdownlint . --fix`
* Manually resolve anything left from `markdownlint .`
Once you push these changes the test should pass, and you can hide this comment :+1:
We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
Thanks again for your contribution!
repo-token: ${{ secrets.GITHUB_TOKEN }}
allow-repeats: false

EditorConfig:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2

- uses: actions/setup-node@v1
with:
node-version: '10'
- uses: actions/setup-node@v2

- name: Install editorconfig-checker
run: npm install -g editorconfig-checker

- name: Run ECLint check
run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
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')

YAML:
Prettier:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v1
- uses: actions/setup-node@v1
with:
node-version: '10'
- name: Install yaml-lint
run: npm install -g yaml-lint
- name: Run yaml-lint
run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml" -o -name "*.yaml")

# If the above check failed, post a comment on the PR explaining the failure
- name: Post PR comment
if: failure()
uses: mshick/add-pr-comment@v1
with:
message: |
## YAML linting is failing
To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:
* Install `yaml-lint`
* [Install `npm`](https://www.npmjs.com/get-npm) then [install `yaml-lint`](https://www.npmjs.com/package/yaml-lint) (`npm install -g yaml-lint`)
* Fix the markdown errors
* Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml")`
* Fix any reported errors in your YAML files
- uses: actions/checkout@v2

Once you push these changes the test should pass, and you can hide this comment :+1:
- uses: actions/setup-node@v2

We highly recommend setting up yaml-lint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
- name: Install Prettier
run: npm install -g prettier

Thanks again for your contribution!
repo-token: ${{ secrets.GITHUB_TOKEN }}
allow-repeats: false
- name: Run Prettier --check
run: prettier --check ${GITHUB_WORKSPACE}

nf-core:
runs-on: ubuntu-latest
steps:

- name: Check out pipeline code
uses: actions/checkout@v2

Expand All @@ -114,8 +50,8 @@ jobs:
- uses: actions/setup-python@v1
with:
python-version: '3.6'
architecture: 'x64'
python-version: "3.6"
architecture: "x64"

- name: Install dependencies
run: |
Expand Down Expand Up @@ -143,3 +79,4 @@ jobs:
lint_results.md
PR_number.txt
#
3 changes: 1 addition & 2 deletions .github/workflows/linting_comment.yml
Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@

name: nf-core linting comment
# This workflow is triggered after the linting action is complete
# It posts an automated comment to the PR, even if the PR is coming from a fork
Expand Down Expand Up @@ -27,4 +26,4 @@ jobs:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
number: ${{ steps.pr_number.outputs.pr_number }}
path: linting-logs/lint_results.md

#
14 changes: 14 additions & 0 deletions .gitpod.yml
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@@ -0,0 +1,14 @@
image: nfcore/gitpod:latest

vscode:
extensions: # based on nf-core.nf-core-extensionpack
- codezombiech.gitignore # Language support for .gitignore files
# - cssho.vscode-svgviewer # SVG viewer
- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
- eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed
- EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
- Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
- mechatroner.rainbow-csv # Highlight columns in csv files in different colors
# - nextflow.nextflow # Nextflow syntax highlighting
- oderwat.indent-rainbow # Highlight indentation level
- streetsidesoftware.code-spell-checker # Spelling checker for source code
14 changes: 0 additions & 14 deletions .markdownlint.yml

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