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include MiXCR toolkit in nf-core/airrflow #1261

include MiXCR toolkit in nf-core/airrflow

include MiXCR toolkit in nf-core/airrflow #1261

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: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/airrflow') }}
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "23.04.0"
- "latest-everything"
steps:
- name: Check out pipeline code
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
- name: Install Nextflow
uses: nf-core/setup-nextflow@v2
with:
version: "${{ matrix.NXF_VER }}"
- name: Disk space cleanup
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
- name: Run pipeline with test data
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
test_profile:
name: Run workflow test with different profiles
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/airrflow') }}
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "23.04.0"
- "latest-everything"
profile:
[
"test_tcr",
"test_no_umi",
"test_nocluster",
"test_fetchimgt",
"test_assembled_hs",
"test_assembled_mm",
"test_10x_sc",
"test_mixcr_bulk",
"test_mixcr_sc",
"test_clontech_umi",
"test_nebnext_umi",
"test_rnaseq_bulk",
"test_rnaseq_sc",
]
fail-fast: false
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"
- name: Run pipeline with test data
run: |
nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker --outdir ./results
- name: Upload logs on failure
if: failure()
uses: actions/upload-artifact@v4
with:
name: logs-${{ matrix.profile }}
path: |
/home/runner/.nextflow.log
/home/runner/work
!/home/runner/work/conda
!/home/runner/work/singularity