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add dorado

add dorado #685

Workflow file for this run

name: nf-core CI
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
on:
push:
branches:
- dev
pull_request:
release:
types: [published]
env:
NXF_ANSI_LOG: false
concurrency:
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
cancel-in-progress: true
jobs:
test:
name: Run pipeline with test data
# Only run on push if this is the nf-core dev branch (merged PRs)
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nanoseq') }}"
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "22.10.1"
- "latest-everything"
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"
- name: Run pipeline with test data
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
profile:
name: Run profile tests
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nanoseq') }}"
runs-on: ubuntu-latest
env:
NXF_VER: "22.10.3"
NXF_ANSI_LOG: false
strategy:
matrix:
profiles:
- "test_bc_nodx"
- "test_nobc_dx"
- "test_nobc_nodx_vc"
- "test_nobc_nodx_stringtie"
- "test_nobc_nodx_noaln"
- "test_nobc_nodx_rnamod"
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"
- name: Run pipeline with different profiles
run: |
nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profiles }},docker --outdir ./results
parameters:
name: Run parameter tests
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nanoseq') }}"
runs-on: ubuntu-latest
env:
NXF_VER: "22.10.3"
NXF_ANSI_LOG: false
strategy:
matrix:
parameters:
- "--aligner graphmap2"
- "--skip_alignment"
- "--skip_qc"
- "--skip_quantification"
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
- name: Install Nextflow
env:
CAPSULE_LOG: none
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Run pipeline with different parameters
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }}
#