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Template update nf-core tools v2.14.1 #133

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May 17, 2024
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2 changes: 1 addition & 1 deletion .github/PULL_REQUEST_TEMPLATE.md
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/baca
- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/bacass/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/bacass _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
- [ ] Make sure your code lints (`nf-core lint`).
- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
- [ ] 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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10 changes: 5 additions & 5 deletions .github/workflows/awsfulltest.yml
Original file line number Diff line number Diff line change
Expand Up @@ -8,12 +8,12 @@ on:
types: [published]
workflow_dispatch:
jobs:
run-tower:
run-platform:
name: Run AWS full tests
if: github.repository == 'nf-core/bacass'
runs-on: ubuntu-latest
steps:
- name: Launch workflow via tower
- 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)
# on the `test_full.config` test runs with only one set of parameters
Expand All @@ -32,7 +32,7 @@ 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
12 changes: 6 additions & 6 deletions .github/workflows/awstest.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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/bacass'
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 }}
Expand All @@ -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
Expand Up @@ -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 }}"

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7 changes: 5 additions & 2 deletions .github/workflows/download_pipeline.yml
Original file line number Diff line number Diff line change
Expand Up @@ -32,9 +32,12 @@ jobs:
- name: Install Nextflow
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:
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6 changes: 3 additions & 3 deletions .github/workflows/fix-linting.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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 }}

Expand All @@ -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
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19 changes: 9 additions & 10 deletions .github/workflows/linting.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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: |
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/linting_comment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/release-announcements.yml
Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ jobs:
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
Expand Down
1 change: 1 addition & 0 deletions .nf-core.yml
Original file line number Diff line number Diff line change
Expand Up @@ -8,3 +8,4 @@ lint:
nextflow_config:
- config_defaults:
- params.dfast_config
nf_core_version: "2.14.1"
3 changes: 3 additions & 0 deletions .pre-commit-config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down
2 changes: 2 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Added`

- [#133](https://github.com/nf-core/bacass/pull/133) Update nf-core/bacass to the new nf-core 2.14.1 `TEMPLATE`.

### `Fixed`

- [#125](https://github.com/nf-core/bacass/pull/125) - Fixed conflicting settings in save_trimmed_fail parameter.
Expand Down
2 changes: 1 addition & 1 deletion README.md
Original file line number Diff line number Diff line change
Expand Up @@ -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/bacass)
[![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/bacass)

[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23bacass-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/bacass)[![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)

Expand Down
3 changes: 0 additions & 3 deletions conf/base.config
Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,4 @@ process {
errorStrategy = 'retry'
maxRetries = 3
}
withName:CUSTOM_DUMPSOFTWAREVERSIONS {
cache = false
}
}
2 changes: 1 addition & 1 deletion conf/test.config
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ params {
max_time = '6.h'

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/bacass/bacass_short.tsv'
input = params.pipelines_testdata_base_path + 'bacass/bacass_short.tsv'

// some extra args to speed tests up
unicycler_args = "--no_correct --no_pilon"
Expand Down
2 changes: 1 addition & 1 deletion conf/test_dfast.config
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ params {
max_time = 6.h

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/bacass/bacass_short.tsv'
input = params.pipelines_testdata_base_path + 'bacass/bacass_short.tsv'

// some extra args to speed tests up
unicycler_args = "--no_correct --no_pilon"
Expand Down
2 changes: 1 addition & 1 deletion conf/test_full.config
Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,6 @@ params {
config_profile_description = 'Full test dataset to check pipeline function'

// Input data for full size test
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/bacass/bacass_full.tsv'
input = params.pipelines_testdata_base_path + 'bacass/bacass_full.tsv'
kraken2db = 'https://genome-idx.s3.amazonaws.com/kraken/k2_standard_8gb_20210517.tar.gz'
}
2 changes: 1 addition & 1 deletion conf/test_hybrid.config
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ params {
max_time = 6.h

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/bacass/bacass_hybrid.tsv'
input = params.pipelines_testdata_base_path + 'bacass/bacass_hybrid.tsv'

// some extra args to speed tests up
assembly_type = 'hybrid'
Expand Down
2 changes: 1 addition & 1 deletion conf/test_hybrid_dragonflye.config
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ params {
max_time = 6.h

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/bacass/bacass_hybrid_dragonflye.tsv'
input = params.pipelines_testdata_base_path + 'bacass/bacass_hybrid_dragonflye.tsv'

// some extra args to speed tests up
assembly_type = 'hybrid'
Expand Down
2 changes: 1 addition & 1 deletion conf/test_long.config
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ params {
max_time = 6.h

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/bacass/bacass_long_miniasm.tsv'
input = params.pipelines_testdata_base_path + 'bacass/bacass_long_miniasm.tsv'

// some extra args to speed tests up
prokka_args = " --fast"
Expand Down
2 changes: 1 addition & 1 deletion conf/test_long_dragonflye.config
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ params {
config_profile_description = 'Minimal test dataset to check pipeline function'

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/bacass/bacass_long_miniasm.tsv'
input = params.pipelines_testdata_base_path + 'bacass/bacass_long_miniasm.tsv'

// some extra args to speed tests up
prokka_args = " --fast"
Expand Down
2 changes: 1 addition & 1 deletion conf/test_long_miniasm.config
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ params {
max_time = 6.h

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/bacass/bacass_long_miniasm.tsv'
input = params.pipelines_testdata_base_path + 'bacass/bacass_long_miniasm.tsv'

// some extra args to speed tests up
prokka_args = " --fast"
Expand Down
2 changes: 2 additions & 0 deletions docs/usage.md
Original file line number Diff line number Diff line change
Expand Up @@ -141,6 +141,8 @@ 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.

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4 changes: 2 additions & 2 deletions modules.json
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@
},
"fastqc": {
"branch": "master",
"git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c",
"git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
"installed_by": ["fastq_trim_fastp_fastqc"]
},
"gunzip": {
Expand Down Expand Up @@ -118,7 +118,7 @@
},
"utils_nfcore_pipeline": {
"branch": "master",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
"git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
"installed_by": ["subworkflows"]
},
"utils_nfvalidation_plugin": {
Expand Down
6 changes: 6 additions & 0 deletions modules/nf-core/fastqc/main.nf

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