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include MiXCR toolkit in nf-core/airrflow #298

include MiXCR toolkit in nf-core/airrflow

include MiXCR toolkit in nf-core/airrflow #298

Workflow file for this run

name: Immcantation
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
on:
pull_request:
branches-ignore:
- "master"
env:
NXF_ANSI_LOG: false
concurrency:
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
cancel-in-progress: true
jobs:
test_container:
name: Run workflow with immcantation devel test_container
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/airrflow') }}
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "23.04.0"
- "latest-everything"
profile:
[
"test_assembled_immcantation_devel_hs",
"test_assembled_immcantation_devel_mm",
"test_raw_immcantation_devel",
]
fail-fast: false
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "${{ 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