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nschcolnicov committed Oct 8, 2024
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4 changes: 4 additions & 0 deletions .editorconfig
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Expand Up @@ -11,6 +11,7 @@ indent_style = space
[*.{md,yml,yaml,html,css,scss,js}]
indent_size = 2


# These files are edited and tested upstream in nf-core/modules
[/modules/nf-core/**]
charset = unset
Expand All @@ -25,9 +26,12 @@ insert_final_newline = unset
trim_trailing_whitespace = unset
indent_style = unset



[/assets/email*]
indent_size = unset


# ignore python and markdown
[*.{py,md}]
indent_style = unset
10 changes: 5 additions & 5 deletions .github/CONTRIBUTING.md
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Expand Up @@ -19,7 +19,7 @@ If you'd like to write some code for nf-core/smrnaseq, the standard workflow is
1. Check that there isn't already an issue about your idea in the [nf-core/smrnaseq issues](https://github.com/nf-core/smrnaseq/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/smrnaseq repository](https://github.com/nf-core/smrnaseq) 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).
4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged

If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
Expand All @@ -40,7 +40,7 @@ There are typically two types of tests that run:
### Lint tests

`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to.
To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command.
To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint <pipeline-directory>` command.

If any failures or warnings are encountered, please follow the listed URL for more documentation.

Expand Down Expand Up @@ -75,7 +75,7 @@ If you wish to contribute a new step, please use the following coding standards:
2. Write the process block (see below).
3. Define the output channel if needed (see below).
4. Add any new parameters to `nextflow.config` with a default (see below).
5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool).
5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool).
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`.
Expand All @@ -86,7 +86,7 @@ If you wish to contribute a new step, please use the following coding standards:

Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.

Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`.

### Default processes resource requirements

Expand All @@ -103,7 +103,7 @@ Please use the following naming schemes, to make it easy to understand what is g

### Nextflow version bumping

If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]`
If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]`

### Images and figures

Expand Down
4 changes: 2 additions & 2 deletions .github/PULL_REQUEST_TEMPLATE.md
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Expand Up @@ -17,8 +17,8 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/smrn
- [ ] 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/smrnaseq/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/smrnaseq _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 (`nf-test test --tag pipeline --profile +docker`).
- [ ] Make sure your code lints (`nf-core pipelines 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.
Expand Down
23 changes: 19 additions & 4 deletions .github/workflows/awsfulltest.yml
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@@ -1,18 +1,33 @@
name: nf-core AWS full size tests
# This workflow is triggered on published releases.
# This workflow is triggered on PRs opened against the master branch.
# It can be additionally triggered manually with GitHub actions workflow dispatch button.
# It runs the -profile 'test_full' on AWS batch

on:
release:
types: [published]
pull_request:
branches:
- master
workflow_dispatch:
pull_request_review:
types: [submitted]

jobs:
run-platform:
name: Run AWS full tests
if: github.repository == 'nf-core/smrnaseq'
if: github.repository == 'nf-core/smrnaseq' && github.event.review.state == 'approved'
runs-on: ubuntu-latest
steps:
- uses: octokit/[email protected]
id: check_approvals
with:
route: GET /repos/${{ github.repository }}/pulls/${{ github.event.review.number }}/reviews
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- id: test_variables
run: |
JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
- name: Launch workflow via Seqera Platform
uses: seqeralabs/action-tower-launch@v2
# Add full size test data (but still relatively small datasets for few samples)
Expand Down
4 changes: 3 additions & 1 deletion .github/workflows/ci.yml
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Expand Up @@ -11,6 +11,7 @@ on:
- master
release:
types: [published]
workflow_dispatch:

env:
NXF_ANSI_LOG: false
Expand All @@ -34,7 +35,8 @@ jobs:
matrix:
shard: [1, 2, 3, 4]
NXF_VER:
- "23.10.4"
- "24.04.2"
- "latest-everything"
profile: ["docker"]
env:
SHARDS: "4"
Expand Down
53 changes: 43 additions & 10 deletions .github/workflows/download_pipeline.yml
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@@ -1,4 +1,4 @@
name: Test successful pipeline download with 'nf-core download'
name: Test successful pipeline download with 'nf-core pipelines download'

# Run the workflow when:
# - dispatched manually
Expand All @@ -8,7 +8,7 @@ on:
workflow_dispatch:
inputs:
testbranch:
description: "The specific branch you wish to utilize for the test execution of nf-core download."
description: "The specific branch you wish to utilize for the test execution of nf-core pipelines download."
required: true
default: "dev"
pull_request:
Expand Down Expand Up @@ -39,9 +39,11 @@ jobs:
with:
python-version: "3.12"
architecture: "x64"
- uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7

- name: Setup Apptainer
uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0
with:
singularity-version: 3.8.3
apptainer-version: 1.3.4

- name: Install dependencies
run: |
Expand All @@ -54,33 +56,64 @@ jobs:
echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
- name: Make a cache directory for the container images
run: |
mkdir -p ./singularity_container_images
- name: Download the pipeline
env:
NXF_SINGULARITY_CACHEDIR: ./
NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
run: |
nf-core download ${{ env.REPO_LOWERCASE }} \
nf-core pipelines 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-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \
--container-cache-utilisation 'amend' \
--download-configuration
--download-configuration 'yes'
- name: Inspect download
run: tree ./${{ env.REPOTITLE_LOWERCASE }}

- name: Count the downloaded number of container images
id: count_initial
run: |
image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
echo "Initial container image count: $image_count"
echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV}
- name: Run the downloaded pipeline (stub)
id: stub_run_pipeline
continue-on-error: true
env:
NXF_SINGULARITY_CACHEDIR: ./
NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
NXF_SINGULARITY_HOME_MOUNT: true
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity,illumina --outdir ./results
- name: Run the downloaded pipeline (stub run not supported)
id: run_pipeline
if: ${{ job.steps.stub_run_pipeline.status == failure() }}
env:
NXF_SINGULARITY_CACHEDIR: ./
NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
NXF_SINGULARITY_HOME_MOUNT: true
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results

- name: Count the downloaded number of container images
id: count_afterwards
run: |
image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
echo "Post-pipeline run container image count: $image_count"
echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV}
- name: Compare container image counts
run: |
if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then
initial_count=${{ env.IMAGE_COUNT_INITIAL }}
final_count=${{ env.IMAGE_COUNT_AFTER }}
difference=$((final_count - initial_count))
echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!"
tree ./singularity_container_images
exit 1
else
echo "The pipeline can be downloaded successfully!"
fi
23 changes: 19 additions & 4 deletions .github/workflows/linting.yml
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
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
# It runs the `nf-core pipelines lint` and markdown lint tests to ensure
# that the code meets the nf-core guidelines.
on:
push:
Expand Down Expand Up @@ -41,17 +41,32 @@ jobs:
python-version: "3.12"
architecture: "x64"

- name: read .nf-core.yml
uses: pietrobolcato/[email protected]
id: read_yml
with:
config: ${{ github.workspace }}/.nf-core.yaml

- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install nf-core
pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
- name: Run nf-core pipelines lint
if: ${{ github.base_ref != 'master' }}
env:
GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md

- name: Run nf-core lint
- name: Run nf-core pipelines lint --release
if: ${{ github.base_ref == 'master' }}
env:
GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md

- name: Save PR number
if: ${{ always() }}
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/linting_comment.yml
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Expand Up @@ -11,7 +11,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Download lint results
uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6
with:
workflow: linting.yml
workflow_conclusion: completed
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/release-announcements.yml
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Expand Up @@ -12,7 +12,7 @@ jobs:
- name: get topics and convert to hashtags
id: get_topics
run: |
echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" >> $GITHUB_OUTPUT
echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT
- uses: rzr/fediverse-action@master
with:
Expand Down
43 changes: 43 additions & 0 deletions .github/workflows/template_version_comment.yml
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@@ -0,0 +1,43 @@
name: nf-core template version comment
# This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version.
# It posts a comment to the PR, even if it comes from a fork.

on: pull_request_target

jobs:
template_version:
runs-on: ubuntu-latest
steps:
- name: Check out pipeline code
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

- name: Read template version from .nf-core.yml
uses: pietrobolcato/[email protected]
id: read_yml
with:
config: ${{ github.workspace }}/.nf-core.yml

- name: Install nf-core
run: |
python -m pip install --upgrade pip
pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
- name: Check nf-core outdated
id: nf_core_outdated
run: pip list --outdated | grep nf-core

- name: Post nf-core template version comment
uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
if: |
${{ steps.nf_core_outdated.outputs.stdout }} =~ 'nf-core'
with:
repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
allow-repeats: false
message: |
## :warning: Newer version of the nf-core template is available.
Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}.
Please update your pipeline to the latest version.
For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
#
7 changes: 2 additions & 5 deletions .gitpod.yml
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Expand Up @@ -4,17 +4,14 @@ tasks:
command: |
pre-commit install --install-hooks
nextflow self-update
- name: unset JAVA_TOOL_OPTIONS
command: |
unset JAVA_TOOL_OPTIONS
vscode:
extensions: # based on nf-core.nf-core-extensionpack
- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
#- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
- 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
- nextflow.nextflow # Nextflow syntax highlighting
- oderwat.indent-rainbow # Highlight indentation level
- streetsidesoftware.code-spell-checker # Spelling checker for source code
- charliermarsh.ruff # Code linter Ruff
17 changes: 15 additions & 2 deletions .nf-core.yml
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@@ -1,6 +1,19 @@
repository_type: pipeline
nf_core_version: "2.14.1"
bump_version: null
lint:
nextflow_config:
- config_defaults:
- params.fastp_known_mirna_adapters
nf_core_version: 3.0.0
org_path: null
repository_type: pipeline
template:
author: "P. Ewels, C. Wang, R. Hammar\xE9n, L. Pantano, A. Peltzer"
description: Small RNA-Seq Best Practice Analysis Pipeline.
force: false
is_nfcore: true
name: smrnaseq
org: nf-core
outdir: .
skip_features: null
version: 2.4.0
update: null
2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
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Expand Up @@ -7,7 +7,7 @@ repos:
- [email protected]

- repo: https://github.com/editorconfig-checker/editorconfig-checker.python
rev: "2.7.3"
rev: "3.0.3"
hooks:
- id: editorconfig-checker
alias: ec
1 change: 1 addition & 0 deletions .prettierignore
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@@ -1,3 +1,4 @@

email_template.html
adaptivecard.json
slackreport.json
Expand Down
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