Skip to content

Commit

Permalink
Merge pull request #2349 from nf-core/dev
Browse files Browse the repository at this point in the history
Dev -> Master for v2.9
  • Loading branch information
mirpedrol authored Jun 30, 2023
2 parents 0912990 + d74b909 commit e5ce6ce
Show file tree
Hide file tree
Showing 97 changed files with 4,895 additions and 3,496 deletions.
1 change: 0 additions & 1 deletion .github/CONTRIBUTING.md
Original file line number Diff line number Diff line change
Expand Up @@ -142,4 +142,3 @@ To get started:
Devcontainer specs:

- [DevContainer config](.devcontainer/devcontainer.json)
- [Dockerfile](.devcontainer/Dockerfile)
2 changes: 1 addition & 1 deletion .github/ISSUE_TEMPLATE/bug_report.yml
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ 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)_
* OS _(eg. CentOS Linux, macOS, Linux Mint)_
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/create-lint-wf.yml
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ jobs:
strategy:
matrix:
NXF_VER:
- "22.10.1"
- "23.04.0"
- "latest-everything"
steps:
# Get the repo code
Expand Down
137 changes: 137 additions & 0 deletions .github/workflows/create-test-lint-wf-template.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,137 @@
name: Create a pipeline from a template and test it
on:
push:
branches:
- dev
paths:
- nf_core/pipeline-template/**
pull_request:
release:
types: [published]

# Cancel if a newer run is started
concurrency:
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
cancel-in-progress: true

env:
NXF_ANSI_LOG: false

jobs:
RunTestWorkflow:
runs-on: ubuntu-latest
env:
NXF_ANSI_LOG: false
strategy:
matrix:
TEMPLATE:
- "template_skip_all.yml"
- "template_skip_github_badges.yml"
- "template_skip_igenomes.yml"
- "template_skip_ci.yml"
- "template_skip_nf_core_configs.yml"

steps:
- uses: actions/checkout@v3
name: Check out source-code repository

- name: Set up Python 3.8
uses: actions/setup-python@v4
with:
python-version: 3.8

- name: Install python dependencies
run: |
python -m pip install --upgrade pip
pip install .
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: latest-everything

# Install the Prettier linting tools
- uses: actions/setup-node@v3

- name: Install Prettier
run: npm install -g prettier

# Install the editorconfig linting tools
- name: Install editorconfig-checker
run: npm install -g editorconfig-checker

# Create template files
- name: Create template skip all (except github)
run: |
printf "prefix: my-prefix\nskip: ['ci', 'github_badges', 'igenomes', 'nf_core_configs']" > template_skip_all.yml
- name: Create template skip github_badges
run: |
printf "prefix: my-prefix\nskip: github_badges" > template_skip_github_badges.yml
- name: Create template skip igenomes
run: |
printf "prefix: my-prefix\nskip: igenomes" > template_skip_igenomes.yml
- name: Create template skip ci
run: |
printf "prefix: my-prefix\nskip: ci" > template_skip_ci.yml
- name: Create template skip nf_core_configs
run: |
printf "prefix: my-prefix\nskip: nf_core_configs" > template_skip_nf_core_configs.yml
# Create a pipeline from the template
- name: create a pipeline from the template ${{ matrix.TEMPLATE }}
run: |
nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml ${{ matrix.TEMPLATE }}
- name: run the pipeline
run: |
nextflow run my-prefix-testpipeline -profile test,docker --outdir ./results
# Remove results folder before linting
- name: remove results folder
run: |
rm -rf ./results
# Try syncing it before we change anything
- name: nf-core sync
run: nf-core --log-file log.txt sync --dir my-prefix-testpipeline/ --template-yaml ${{ matrix.TEMPLATE }}

# Run code style linting
- name: Run Prettier --check
run: prettier --check my-prefix-testpipeline

- name: Run ECLint check
run: editorconfig-checker -exclude README.md $(find my-prefix-testpipeline/.* -type f | grep -v '.git\|.py\|md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')

# Remove TODO statements
- name: remove TODO
run: find my-prefix-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \;

# Replace zenodo.XXXXXX to pass readme linting
- name: replace zenodo.XXXXXX
run: find my-prefix-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \;

# Run nf-core linting
- name: nf-core lint
run: nf-core --log-file log.txt --hide-progress lint --dir my-prefix-testpipeline --fail-warned

# Run bump-version
- name: nf-core bump-version
run: nf-core --log-file log.txt bump-version --dir my-prefix-testpipeline/ 1.1

# Run nf-core linting in release mode
- name: nf-core lint in release mode
run: nf-core --log-file log.txt --hide-progress lint --dir my-prefix-testpipeline --fail-warned --release

- name: Tar files
run: tar -cvf artifact_files.tar log.txt template_skip*.yml

- name: Upload log file artifact
if: ${{ always() }}
uses: actions/upload-artifact@v3
with:
name: nf-core-log-file
path: artifact_files.tar
2 changes: 1 addition & 1 deletion .github/workflows/create-test-wf.yml
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ jobs:
strategy:
matrix:
NXF_VER:
- "22.10.1"
- "23.04.0"
- "latest-everything"
steps:
- uses: actions/checkout@v3
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/pytest-frozen-ubuntu-20.04.yml
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ concurrency:
cancel-in-progress: true

jobs:
pytest:
pytest-frozen:
runs-on: ubuntu-20.04
steps:
- uses: actions/checkout@v3
Expand Down
1 change: 1 addition & 0 deletions .gitpod.yml
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ tasks:
python -m pip install -e .
python -m pip install -r requirements-dev.txt
pre-commit install --install-hooks
nextflow self-update
vscode:
extensions: # based on nf-core.nf-core-extensionpack
- codezombiech.gitignore # Language support for .gitignore files
Expand Down
68 changes: 68 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -1,5 +1,73 @@
# nf-core/tools: Changelog

# [v2.9 - Chromium Falcon](https://github.com/nf-core/tools/releases/tag/2.9) + [2023-06-29]

### Template

- `params.max_multiqc_email_size` is no longer required ([#2273](https://github.com/nf-core/tools/pull/2273))
- Remove `cleanup = true` from `test_full.config` in pipeline template ([#2279](https://github.com/nf-core/tools/pull/2279))
- Fix usage docs for specifying `params.yaml` ([#2279](https://github.com/nf-core/tools/pull/2279))
- Added stub in modules template ([#2277])(https://github.com/nf-core/tools/pull/2277) [Contributed by @nvnieuwk]
- Move registry definitions out of profile scope ([#2286])(https://github.com/nf-core/tools/pull/2286)
- Remove `aws_tower` profile ([#2287])(https://github.com/nf-core/tools/pull/2287)
- Fixed the Slack report to include the pipeline name ([#2291](https://github.com/nf-core/tools/pull/2291))
- Fix link in the MultiQC report to point to exact version of output docs ([#2298](https://github.com/nf-core/tools/pull/2298))
- Updates seqeralabs/action-tower-launch to v2.0.0 ([#2301](https://github.com/nf-core/tools/pull/2301))
- Remove schema validation from `lib` folder and use Nextflow [nf-validation plugin](https://nextflow-io.github.io/nf-validation/) instead ([#1771](https://github.com/nf-core/tools/pull/1771/))
- Fix parsing of container directive when it is not typical nf-core format ([#2306](https://github.com/nf-core/tools/pull/2306))
- Add ability to specify custom registry for linting modules, defaults to quay.io ([#2313](https://github.com/nf-core/tools/pull/2313))
- Add `singularity.registry = 'quay.io'` in pipeline template ([#2305](https://github.com/nf-core/tools/pull/2305))
- Add `apptainer.registry = 'quay.io'` in pipeline template ([#2352](https://github.com/nf-core/tools/pull/2352))
- Bump minimum required NF version in pipeline template from `22.10.1` -> `23.04.0` ([#2305](https://github.com/nf-core/tools/pull/2305))
- Add ability to interpret `docker.registry` from `nextflow.config` file. If not found defaults to quay.io. ([#2318](https://github.com/nf-core/tools/pull/2318))
- Add functions to dynamically include pipeline tool citations in MultiQC methods description section for better reporting. ([#2326](https://github.com/nf-core/tools/pull/2326))
- Remove `--tracedir` parameter ([#2290](https://github.com/nf-core/tools/pull/2290))
- Incorrect config parameter warnings when customising pipeline template ([#2333](https://github.com/nf-core/tools/pull/2333))
- Use markdown syntax in the description for the meta map channels ([#2358](https://github.com/nf-core/tools/pull/2358))

### Download

- Introduce a `--tower` flag for `nf-core download` to obtain pipelines in an offline format suited for [seqeralabs® Nextflow Tower](https://cloud.tower.nf/) ([#2247](https://github.com/nf-core/tools/pull/2247)).
- Refactored the CLI for `--singularity-cache` in `nf-core download` from a flag to an argument. The prior options were renamed to `amend` (container images are only saved in the `$NXF_SINGULARITY_CACHEDIR`) and `copy` (a copy of the image is saved with the download). `remote` was newly introduced and allows to provide a table of contents of a remote cache via an additional argument `--singularity-cache-index` ([#2247](https://github.com/nf-core/tools/pull/2247)).
- Refactored the CLI parameters related to container images. Although downloading other images than those of the Singularity/Apptainer container system is not supported for the time being, a generic name for the parameters seemed preferable. So the new parameter `--singularity-cache-index` introduced in [#2247](https://github.com/nf-core/tools/pull/2247) has been renamed to `--container-cache-index` prior to release ([#2336](https://github.com/nf-core/tools/pull/2336)).
- To address issue [#2311](https://github.com/nf-core/tools/issues/2311), a new parameter `--container-library` was created allowing to specify the container library (registry) from which container images in OCI format (Docker) should be pulled ([#2336](https://github.com/nf-core/tools/pull/2336)).
- Container detection in configs was improved. This allows for DSL2-like container definitions inside the container parameter value provided to process scopes [#2346](https://github.com/nf-core/tools/pull/2346).
- Add apptainer to the list of false positve container strings ([#2353](https://github.com/nf-core/tools/pull/2353)).

#### Updated CLI parameters

| Old parameter | New parameter |
| --------------------- | ---------------------------------------------- |
| new parameter | `-d` / `--download-configuration` |
| new parameter | `-t` / `--tower` |
| `-c`/ `--container` | `-s` / `--container-system <VALUE>` |
| new parameter | `-l` / `--container-library <VALUE>` |
| `--singularity-cache` | `-u` / `--container-cache-utilisation <VALUE>` |
| new parameter | `-i` / `--container-cache-index <VALUE>` |

_In addition, `-r` / `--revision` has been changed to a parameter that can be provided multiple times so several revisions can be downloaded at once._

### Linting

- Warn if container access is denied ([#2270](https://github.com/nf-core/tools/pull/2270))
- Error if module container specification has quay.io as prefix when it shouldn't have ([#2278])(https://github.com/nf-core/tools/pull/2278/files)
- Detect if container is 'simple name' and try to contact quay.io server by default ([#2281](https://github.com/nf-core/tools/pull/2281))
- Warn about null/None/empty default values in `nextflow_schema.json` ([#3328](https://github.com/nf-core/tools/pull/2328))
- Fix linting when creating a pipeline skipping some parts of the template and add CI test ([#2330](https://github.com/nf-core/tools/pull/2330))

### Modules

- Don't update `modules_json` object if a module is not updated ([#2323](https://github.com/nf-core/tools/pull/2323))

### Subworkflows

### General

- GitPod base image: Always self-update to the latest version of Nextflow. Add [pre-commit](https://pre-commit.com/) dependency.
- GitPod configs: Update Nextflow as an init task, init pre-commit in pipeline config.
- Refgenie: Create `nxf_home/nf-core/refgenie_genomes.config` path if it doesn't exist ([#2312](https://github.com/nf-core/tools/pull/2312))
- Add CI tests to test running a pipeline whe it's created from a template skipping different areas

# [v2.8 - Ruthenium Monkey](https://github.com/nf-core/tools/releases/tag/2.8) - [2023-04-27]

### Template
Expand Down
Loading

0 comments on commit e5ce6ce

Please sign in to comment.