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latest-dry-run

latest-dry-run #2

Workflow file for this run

name: immediate_1
on: workflow_dispatch
env:
ASSCOM2_PROFILE: "profile/conda/local"
jobs:
create-env:
name: ${{ matrix.os }}
runs-on: ${{ matrix.os }}
defaults:
run:
shell: bash -l {0}
strategy:
fail-fast: false
matrix:
os: [ubuntu-latest]
steps:
- name: checkout repository
uses: actions/checkout@v2
- name: create environment with mamba
uses: conda-incubator/setup-miniconda@v2
with:
mamba-version: "*"
channels: conda-forge,bioconda,defaults
auto-activate-base: false
activate-environment: asscom2
environment-file: environment.yaml
- name: check solution
run: |
mamba env export
- name: test installation
run: |
./asscom2 --version
./asscom2 --help
- name: dry run
run: |
./asscom2 --config input_genomes="tests/E._faecium/*.fna" --dry-run
- name: setup conda envs and copy
run: |
./asscom2 --config input_genomes="tests/E._faecium/*.fna" --until copy && mamba clean --all -y
- name: fast
run: |
./asscom2 --config input_genomes="tests/E._faecium/*.fna" --until fast