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Merge template 2.14.1 #155

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May 15, 2024
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6 changes: 1 addition & 5 deletions .editorconfig
Original file line number Diff line number Diff line change
@@ -28,10 +28,6 @@ indent_style = unset
[/assets/email*]
indent_size = unset

# ignore Readme
[README.md]
indent_style = unset

# ignore python
# ignore python and markdown
[*.{py,md}]
indent_style = unset
2 changes: 1 addition & 1 deletion .github/PULL_REQUEST_TEMPLATE.md
Original file line number Diff line number Diff line change
@@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/prot
- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/proteinfold/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/proteinfold _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 main.nf.test -profile test,docker`).
- [ ] 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.
12 changes: 6 additions & 6 deletions .github/workflows/awsfulltest.yml
Original file line number Diff line number Diff line change
@@ -8,8 +8,8 @@ on:
types: [published]
workflow_dispatch:
jobs:
run-tower:
name: Run AWS AlphaFold2 full monomer tests
run-platform:
name: Run AWS full tests
if: github.repository == 'nf-core/proteinfold'
runs-on: ubuntu-latest
# Do a full-scale run on each of the mode
@@ -27,7 +27,7 @@ jobs:
"_esmfold_multimer",
]
steps:
- name: Launch workflow via tower
- name: Launch workflow via Seqera Platform
uses: seqeralabs/action-tower-launch@v2
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
@@ -43,7 +43,7 @@ jobs:
profiles: test_full_${{ matrix.mode }},aws_tower
- uses: actions/upload-artifact@v4
with:
name: Tower debug log file
name: Seqera Platform debug log file
path: |
tower_action_*.log
tower_action_*.json
seqera_platform_action_*.log
seqera_platform_action_*.json
12 changes: 6 additions & 6 deletions .github/workflows/awstest.yml
Original file line number Diff line number Diff line change
@@ -5,13 +5,13 @@ name: nf-core AWS test
on:
workflow_dispatch:
jobs:
run-tower:
run-platform:
name: Run AWS tests
if: github.repository == 'nf-core/proteinfold'
runs-on: ubuntu-latest
steps:
# Launch workflow using Tower CLI tool action
- name: Launch workflow via tower
# Launch workflow using Seqera Platform CLI tool action
- name: Launch workflow via Seqera Platform
uses: seqeralabs/action-tower-launch@v2
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
@@ -27,7 +27,7 @@ jobs:

- uses: actions/upload-artifact@v4
with:
name: Tower debug log file
name: Seqera Platform debug log file
path: |
tower_action_*.log
tower_action_*.json
seqera_platform_action_*.log
seqera_platform_action_*.json
4 changes: 2 additions & 2 deletions .github/workflows/ci.yml
Original file line number Diff line number Diff line change
@@ -28,10 +28,10 @@ jobs:
- "latest-everything"
steps:
- name: Check out pipeline code
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
uses: nf-core/setup-nextflow@v2
with:
version: "${{ matrix.NXF_VER }}"

22 changes: 18 additions & 4 deletions .github/workflows/download_pipeline.yml
Original file line number Diff line number Diff line change
@@ -14,6 +14,8 @@ on:
pull_request:
types:
- opened
- edited
- synchronize
branches:
- master
pull_request_target:
@@ -28,11 +30,14 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
uses: nf-core/setup-nextflow@v2

- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
- name: Disk space cleanup
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1

- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
with:
python-version: "3.11"
python-version: "3.12"
architecture: "x64"
- uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
with:
@@ -65,8 +70,17 @@ jobs:
- name: Inspect download
run: tree ./${{ env.REPOTITLE_LOWERCASE }}

- name: Run the downloaded pipeline
- name: Run the downloaded pipeline (stub)
id: stub_run_pipeline
continue-on-error: true
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
- name: Run the downloaded pipeline (stub run not supported)
id: run_pipeline
if: ${{ job.steps.stub_run_pipeline.status == failure() }}
env:
NXF_SINGULARITY_CACHEDIR: ./
NXF_SINGULARITY_HOME_MOUNT: true
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
6 changes: 3 additions & 3 deletions .github/workflows/fix-linting.yml
Original file line number Diff line number Diff line change
@@ -13,7 +13,7 @@ jobs:
runs-on: ubuntu-latest
steps:
# Use the @nf-core-bot token to check out so we can push later
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
- uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
with:
token: ${{ secrets.nf_core_bot_auth_token }}

@@ -32,9 +32,9 @@ jobs:
GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}

# Install and run pre-commit
- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
with:
python-version: 3.11
python-version: "3.12"

- name: Install pre-commit
run: pip install pre-commit
19 changes: 9 additions & 10 deletions .github/workflows/linting.yml
Original file line number Diff line number Diff line change
@@ -14,13 +14,12 @@ jobs:
pre-commit:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
- uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

- name: Set up Python 3.11
uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
- name: Set up Python 3.12
uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
with:
python-version: 3.11
cache: "pip"
python-version: "3.12"

- name: Install pre-commit
run: pip install pre-commit
@@ -32,14 +31,14 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Check out pipeline code
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
uses: nf-core/setup-nextflow@v2

- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
with:
python-version: "3.11"
python-version: "3.12"
architecture: "x64"

- name: Install dependencies
@@ -60,7 +59,7 @@ jobs:

- name: Upload linting log file artifact
if: ${{ always() }}
uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
with:
name: linting-logs
path: |
2 changes: 1 addition & 1 deletion .github/workflows/linting_comment.yml
Original file line number Diff line number Diff line change
@@ -11,7 +11,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Download lint results
uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
with:
workflow: linting.yml
workflow_conclusion: completed
6 changes: 3 additions & 3 deletions .github/workflows/release-announcements.yml
Original file line number Diff line number Diff line change
@@ -12,7 +12,7 @@ jobs:
- name: get topics and convert to hashtags
id: get_topics
run: |
curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ 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' ' ')" >> $GITHUB_OUTPUT

- uses: rzr/fediverse-action@master
with:
@@ -25,13 +25,13 @@ jobs:

Please see the changelog: ${{ github.event.release.html_url }}

${{ steps.get_topics.outputs.GITHUB_OUTPUT }} #nfcore #openscience #nextflow #bioinformatics
${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics

send-tweet:
runs-on: ubuntu-latest

steps:
- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
with:
python-version: "3.10"
- name: Install dependencies
1 change: 1 addition & 0 deletions .nf-core.yml
Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
repository_type: pipeline
nf_core_version: "2.14.1"
lint:
files_unchanged:
- .github/ISSUE_TEMPLATE/bug_report.yml
3 changes: 3 additions & 0 deletions .pre-commit-config.yaml
Original file line number Diff line number Diff line change
@@ -3,6 +3,9 @@ repos:
rev: "v3.1.0"
hooks:
- id: prettier
additional_dependencies:
- prettier@3.2.5

- repo: https://github.com/editorconfig-checker/editorconfig-checker.python
rev: "2.7.3"
hooks:
1 change: 1 addition & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -33,6 +33,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [[#147](https://github.com/nf-core/proteinfold/issues/147)] - Update modules to last version.
- [[#145](https://github.com/nf-core/proteinfold/issues/145)] - Implement test to check the processes/subworkflows triggered when downloading the databases.
- [[#130](https://github.com/nf-core/proteinfold/issues/130)] - Add `--skip_multiqc` parameter.
- [[PR #154](https://github.com/nf-core/proteinfold/pull/154)] - Update pipeline template to [nf-core/tools 2.14.1](https://github.com/nf-core/tools/releases/tag/2.14.1).
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Suggested change
- [[PR #154](https://github.com/nf-core/proteinfold/pull/154)] - Update pipeline template to [nf-core/tools 2.14.1](https://github.com/nf-core/tools/releases/tag/2.14.1).
- [PR #154](https://github.com/nf-core/proteinfold/pull/154) - Update pipeline template to [nf-core/tools 2.14.1](https://github.com/nf-core/tools/releases/tag/2.14.1).


### Parameters

2 changes: 1 addition & 1 deletion README.md
Original file line number Diff line number Diff line change
@@ -13,7 +13,7 @@
[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/proteinfold)
[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/proteinfold)

[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23proteinfold-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/proteinfold)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)

3 changes: 0 additions & 3 deletions conf/base.config
Original file line number Diff line number Diff line change
@@ -59,7 +59,4 @@ process {
errorStrategy = 'retry'
maxRetries = 2
}
withName:CUSTOM_DUMPSOFTWAREVERSIONS {
cache = false
}
}
8 changes: 0 additions & 8 deletions conf/modules.config
Original file line number Diff line number Diff line change
@@ -20,14 +20,6 @@ process {
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]

withName: 'CUSTOM_DUMPSOFTWAREVERSIONS' {
publishDir = [
path: { "${params.outdir}/pipeline_info" },
mode: params.publish_dir_mode,
pattern: '*_versions.yml'
]
}
}

//
2 changes: 1 addition & 1 deletion conf/test.config
Original file line number Diff line number Diff line change
@@ -24,7 +24,7 @@ params {
// Input data to test alphafold2 analysis
mode = 'alphafold2'
alphafold2_mode = 'standard'
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
input = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
alphafold2_db = "${projectDir}/assets/dummy_db_dir"
}

2 changes: 1 addition & 1 deletion conf/test_alphafold_download.config
Original file line number Diff line number Diff line change
@@ -24,7 +24,7 @@ params {
// Input data to test alphafold2 analysis
mode = 'alphafold2'
alphafold2_mode = 'standard'
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
input = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
}

process {
2 changes: 1 addition & 1 deletion conf/test_alphafold_split.config
Original file line number Diff line number Diff line change
@@ -24,7 +24,7 @@ params {
// Input data to test alphafold2 splitting MSA from prediction analysis
mode = 'alphafold2'
alphafold2_mode = 'split_msa_prediction'
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
input = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
alphafold2_db = "${projectDir}/assets/dummy_db_dir"
}

2 changes: 1 addition & 1 deletion conf/test_colabfold_download.config
Original file line number Diff line number Diff line change
@@ -24,7 +24,7 @@ params {
// Input data to test colabfold analysis
mode = 'colabfold'
colabfold_server = 'webserver'
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
input = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
}

process {
2 changes: 1 addition & 1 deletion conf/test_colabfold_local.config
Original file line number Diff line number Diff line change
@@ -23,7 +23,7 @@ params {
mode = 'colabfold'
colabfold_server = 'local'
colabfold_db = "${projectDir}/assets/dummy_db_dir"
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
input = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
}

process {
2 changes: 1 addition & 1 deletion conf/test_colabfold_webserver.config
Original file line number Diff line number Diff line change
@@ -23,7 +23,7 @@ params {
mode = 'colabfold'
colabfold_server = 'webserver'
colabfold_db = "${projectDir}/assets/dummy_db_dir"
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
input = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
}

process {
2 changes: 1 addition & 1 deletion conf/test_esmfold.config
Original file line number Diff line number Diff line change
@@ -22,7 +22,7 @@ params {
// Input data to test esmfold
mode = 'esmfold'
esmfold_db = "${projectDir}/assets/dummy_db_dir"
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
input = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
}

process {
2 changes: 1 addition & 1 deletion conf/test_full.config
Original file line number Diff line number Diff line change
@@ -17,6 +17,6 @@ params {
// Input data for full test of alphafold standard mode
mode = 'alphafold2'
alphafold2_mode = 'standard'
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
input = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
alphafold2_db = 's3://proteinfold-dataset/test-data/db/alphafold_mini'
}
2 changes: 1 addition & 1 deletion conf/test_full_alphafold_multimer.config
Original file line number Diff line number Diff line change
@@ -18,6 +18,6 @@ params {
mode = 'alphafold2'
alphafold2_mode = 'standard'
alphafold2_model_preset = 'multimer'
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteinfold/testdata/samplesheet/v1.0/samplesheet_multimer.csv'
input = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet_multimer.csv'
alphafold2_db = 's3://proteinfold-dataset/test-data/db/alphafold_mini'
}
2 changes: 1 addition & 1 deletion conf/test_full_alphafold_split.config
Original file line number Diff line number Diff line change
@@ -17,6 +17,6 @@ params {
// Input data to test colabfold with a local server analysis
mode = 'alphafold2'
alphafold2_mode = 'split_msa_prediction'
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
input = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
alphafold2_db = 's3://proteinfold-dataset/test-data/db/alphafold_mini'
}
2 changes: 1 addition & 1 deletion conf/test_full_colabfold_local.config
Original file line number Diff line number Diff line change
@@ -19,7 +19,7 @@ params {
mode = 'colabfold'
colabfold_server = 'local'
colabfold_model_preset = 'alphafold2_ptm'
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
input = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
colabfold_db = 's3://proteinfold-dataset/test-data/db/colabfold_mini'
}
process {
2 changes: 1 addition & 1 deletion conf/test_full_colabfold_webserver.config
Original file line number Diff line number Diff line change
@@ -18,6 +18,6 @@ params {
mode = 'colabfold'
colabfold_server = 'webserver'
colabfold_model_preset = 'alphafold2_ptm'
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
input = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
colabfold_db = 's3://proteinfold-dataset/test-data/db/colabfold_mini'
}
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