Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merge template 2.14.1 #155

Merged
merged 9 commits into from
May 15, 2024
Merged
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
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).
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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'
}
2 changes: 1 addition & 1 deletion conf/test_full_colabfold_webserver_multimer.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_multimer_v3'
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'
colabfold_db = 's3://proteinfold-dataset/test-data/db/colabfold_mini'
}
2 changes: 1 addition & 1 deletion conf/test_full_esmfold.config
Original file line number Diff line number Diff line change
@@ -17,6 +17,6 @@ params {
// Input data for full test of esmfold monomer
mode = 'esmfold'
esmfold_model_preset = 'monomer'
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'
esmfold_db = 's3://proteinfold-dataset/test-data/db/esmfold'
}
2 changes: 1 addition & 1 deletion conf/test_full_esmfold_multimer.config
Original file line number Diff line number Diff line change
@@ -17,6 +17,6 @@ params {
// Input data for full test of esmfold multimer
mode = 'esmfold'
esmfold_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'
esmfold_db = 's3://proteinfold-dataset/test-data/db/esmfold'
}
2 changes: 2 additions & 0 deletions docs/usage.md
Original file line number Diff line number Diff line change
@@ -503,6 +503,8 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
- A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
- `apptainer`
- A generic configuration profile to be used with [Apptainer](https://apptainer.org/)
- `wave`
- A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later).
- `conda`
- A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer.

2 changes: 1 addition & 1 deletion modules.json
Original file line number Diff line number Diff line change
@@ -48,7 +48,7 @@
},
"utils_nfcore_pipeline": {
"branch": "master",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
"git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
"installed_by": ["subworkflows"]
},
"utils_nfvalidation_plugin": {
129 changes: 68 additions & 61 deletions nextflow.config
Original file line number Diff line number Diff line change
@@ -90,15 +90,16 @@ params {
multiqc_methods_description = null

// Boilerplate options
outdir = null
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
version = false
outdir = null
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
version = false
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'

// Config options
config_profile_name = null
@@ -139,33 +140,32 @@ try {
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config/proteinfold profiles: ${params.custom_config_base}/pipeline/proteinfold.config")
}

profiles {
debug {
dumpHashes = true
process.beforeScript = 'echo $HOSTNAME'
cleanup = false
dumpHashes = true
process.beforeScript = 'echo $HOSTNAME'
cleanup = false
nextflow.enable.configProcessNamesValidation = true
}
conda {
conda.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
channels = ['conda-forge', 'bioconda', 'defaults']
apptainer.enabled = false
conda.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
conda.channels = ['conda-forge', 'bioconda', 'defaults']
apptainer.enabled = false
}
mamba {
conda.enabled = true
conda.useMamba = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
conda.enabled = true
conda.useMamba = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
docker {
docker.enabled = true
@@ -201,46 +201,53 @@ profiles {
apptainer.enabled = false
}
podman {
podman.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
podman.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
shifter {
shifter.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
shifter.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
charliecloud {
charliecloud.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
apptainer.enabled = false
charliecloud.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
apptainer.enabled = false
}
apptainer {
apptainer.enabled = true
apptainer.autoMounts = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = true
apptainer.autoMounts = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
wave {
apptainer.ociAutoPull = true
singularity.ociAutoPull = true
wave.enabled = true
wave.freeze = true
wave.strategy = 'conda,container'
}
gitpod {
executor.name = 'local'
executor.cpus = 4
executor.memory = 8.GB
executor.name = 'local'
executor.cpus = 4
executor.memory = 8.GB
}
test { includeConfig 'conf/test.config' }
test_alphafold2_split { includeConfig 'conf/test_alphafold_split.config' }
7 changes: 7 additions & 0 deletions nextflow_schema.json
Original file line number Diff line number Diff line change
@@ -636,6 +636,13 @@
"description": "Validation of parameters in lenient more.",
"hidden": true,
"help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
},
"pipelines_testdata_base_path": {
"type": "string",
"fa_icon": "far fa-check-circle",
"description": "Base URL or local path to location of pipeline test dataset files",
"default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
"hidden": true
}
}
}
15 changes: 0 additions & 15 deletions pyproject.toml

This file was deleted.

16 changes: 14 additions & 2 deletions subworkflows/local/utils_nfcore_proteinfold_pipeline/main.nf
Original file line number Diff line number Diff line change
@@ -104,6 +104,10 @@ workflow PIPELINE_COMPLETION {
imNotification(summary_params, hook_url)
}
}

workflow.onError {
log.error "Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting"
}
}

/*
@@ -175,8 +179,16 @@ def methodsDescriptionText(mqc_methods_yaml) {
meta["manifest_map"] = workflow.manifest.toMap()

// Pipeline DOI
meta["doi_text"] = meta.manifest_map.doi ? "(doi: <a href=\'https://doi.org/${meta.manifest_map.doi}\'>${meta.manifest_map.doi}</a>)" : ""
meta["nodoi_text"] = meta.manifest_map.doi ? "": "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
if (meta.manifest_map.doi) {
// Using a loop to handle multiple DOIs
// Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
// Removing ` ` since the manifest.doi is a string and not a proper list
def temp_doi_ref = ""
String[] manifest_doi = meta.manifest_map.doi.tokenize(",")
for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: <a href=\'https://doi.org/${doi_ref.replace("https://doi.org/", "").replace(" ", "")}\'>${doi_ref.replace("https://doi.org/", "").replace(" ", "")}</a>), "
meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2)
} else meta["doi_text"] = ""
meta["nodoi_text"] = meta.manifest_map.doi ? "" : "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"

// Tool references
meta["tool_citations"] = ""
8 changes: 7 additions & 1 deletion subworkflows/nf-core/utils_nfcore_pipeline/main.nf

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.