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feat: use nf-schema to validate params (CCBR#68)
* feat: use nf-schema to validate params * ci: 📑 update params docs with 'nf-core pipelines schema docs' * chore: update CHANGELOG.md ---------
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‎.github/workflows/auto-format.yml‎

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permissions:
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contents: write
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pull-requests: write
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jobs:
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auto-format:
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if: github.event_name == 'pull_request'
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with:
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fetch-depth: 0
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ref: ${{ github.event.pull_request.head.ref }}
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ref: ${{ github.head_ref }}
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- uses: actions/checkout@v4
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if: github.event_name != 'pull_request'
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with:
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fetch-depth: 0
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- name: format
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- uses: actions/setup-python@v4
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with:
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python-version: 3.11
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- name: Install nextflow
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uses: nf-core/setup-nextflow@v1
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- name: git config
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run: |
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git config --global user.name "github-actions[bot]"
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git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install .[dev]
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- name: Write nf-schema docs
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run: |
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nf-core pipelines schema docs -f -x markdown -o docs/params.tmp
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echo "<!-- This doc is generated by: nf-core pipelines schema docs. Edit parameter descriptions in nextflow_schema.json -->\n" > docs/params.md
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cat docs/params.tmp >> docs/params.md
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rm -f docs/params.tmp
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- name: Format
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uses: pre-commit/action@v3.0.1
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continue-on-error: true
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- name: commit & push
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run: |
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git config --global user.name "github-actions[bot]"
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git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
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git add docs/params.md
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git commit -m "ci: 📑 update params docs with 'nf-core pipelines schema docs'" || echo "nothing to commit"
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git add .
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git commit -m "ci: 🤖 format everything with pre-commit" && git push || echo "nothing to commit"
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git commit -m "ci: 🤖 format everything with pre-commit" || echo "nothing to commit"
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git push || echo "nothing to push"

‎.github/workflows/build.yml‎

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run: |
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python -m pip install --upgrade pip setuptools
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pip install .[dev,test]
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- name: lint nxf
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if: always()
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run: |
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nf-core pipelines schema lint
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- name: Check CLI basics
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run: |
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which crispin

‎.pre-commit-config.yaml‎

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exclude: |
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(?x)(
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^assets/|
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^docs/.*.html
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^docs/.*.html|
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^nextflow_schema.json
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)
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks

‎CHANGELOG.md‎

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## CRISPIN development version
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- Nextflow parameters are now validated at the start of the workflow. (#68, @kelly-sovacool)
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## CRISPIN 1.2.1
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- Improve help message for `crispin run`. (#65, @kelly-sovacool)

‎MANIFEST.in‎

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include README.md
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include main.nf
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include nextflow.config
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include nextflow_schema.json
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exclude *.py[ocd]

‎assets/dag.png‎

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‎conf/biowulf.config‎

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// CCBR shared resource paths
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index_dir = '/data/CCBR_Pipeliner/db/PipeDB/Indices'
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fastq_screen {
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conf = "assets/fastq_screen_biowulf.conf"
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db_dir = '/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen_db/'
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}
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}
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singularity {

‎conf/containers.config‎

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// containers accessed in process definitions with $params.containers.NAME
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// containers accessed in process definitions with $params.container_NAME
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params {
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containers {
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bagel = 'nciccbr/crispin_bagel_2.0:0.1.0'
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base = 'nciccbr/ccbr_ubuntu_base_20.04:v5'
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cutadapt = 'nciccbr/ncigb_cutadapt_v1.18:latest'
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drugz = 'nciccbr/crispin_drugz:0.1.0'
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fastqc = 'nciccbr/ccrgb_qctools:v4.0'
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mageck = 'quay.io/biocontainers/mageck:0.5.9.5--py39h1f90b4d_3'
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vispr = 'quay.io/biocontainers/mageck-vispr:0.5.6--py_0'
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}
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container_bagel = 'nciccbr/crispin_bagel_2.0:0.1.0'
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container_base = 'nciccbr/ccbr_ubuntu_base_20.04:v5'
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container_cutadapt = 'nciccbr/ncigb_cutadapt_v1.18:latest'
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container_drugz = 'nciccbr/crispin_drugz:0.1.0'
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container_fastqc = 'nciccbr/ccrgb_qctools:v4.0'
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container_mageck = 'quay.io/biocontainers/mageck:0.5.9.5--py39h1f90b4d_3'
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container_vispr = 'quay.io/biocontainers/mageck-vispr:0.5.6--py_0'
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}

‎conf/frce.config‎

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// CCBR shared resource paths
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index_dir = null // TODO
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fastq_screen {
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conf = "assets/fastq_screen_frce.conf" // TODO
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db_dir = null // TODO
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}
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}
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singularity {

‎conf/interactive.config‎

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max_cpus = 56
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max_time = '12 h'
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}
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process.scratch = false

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