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Wrap up v3.3.3

Wrap up v3.3.3 #8

name: Testing new PR with docker
on:
pull_request:
branches: [master, dev]
types: [ opened, synchronize, reopened ]
jobs:
run_nextflow:
name: Run pipeline for the upcoming PR
runs-on: ubuntu-latest
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: Clean environment
run: |
sudo rm -rf /usr/local/lib/android # will release about 10 GB if you don't need Android
sudo rm -rf /usr/share/dotnet # will release about 20GB if you don't need .NET
- name: Get database
run: |
nextflow run main.nf -profile docker --get_zenodo_db --output ./zenodo_db --max_memory '6.GB' --max_cpus 2
sudo rm -r work .nextflow*
yes | docker system prune
- name: Run quicktest profile
run: |
nextflow run main.nf -profile docker,quicktest --bacannot_db $( realpath ./zenodo_db/bac* ) --output ./results --max_memory '6.GB' --max_cpus 2
sudo rm -r work .nextflow*
yes | docker system prune
- name: View results
run: |
sudo apt-get install -y tree
tree ./results