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Fix CI test

Fix CI test #1422

Workflow file for this run

name: osx
on: [pull_request, push]
defaults:
run:
shell: bash -l {0}
jobs:
createEnvs_OSX:
strategy:
fail-fast: false
matrix:
envs: [
'CONDA_SHARED_ENV',
'CONDA_CREATE_INDEX_ENV',
'CONDA_RNASEQ_ENV',
'CONDA_RMATS_ENV',
'CONDA_scRNASEQ_ENV',
'CONDA_seurat3_ENV',
'CONDA_loompy_ENV',
'CONDA_alevinqc_ENV',
'CONDA_eisaR_ENV',
'CONDA_DNA_MAPPING_ENV',
'CONDA_CHIPSEQ_ENV',
'CONDA_ATAC_ENV',
'CONDA_HIC_ENV',
'CONDA_WGBS_ENV',
'CONDA_DSS_ENV',
'CONDA_RMD_ENV',
'CONDA_PREPROCESSING_ENV',
'CONDA_NONCODING_RNASEQ_ENV',
'CONDA_SAMBAMBA_ENV',
'CONDA_pysam_ENV'
]
runs-on: macos-latest
steps:
- uses: actions/checkout@v4
- uses: conda-incubator/setup-miniconda@v3
with:
environment-file: .github/conda_ci.yml
activate-environment: conda_ci
condarc-file: .github/condarc.yml
- name: install snakePipes_OSX
run: |
pip install .
- name: createEnvsOSX
run: |
conda config --add subdirs osx-64
snakePipes createEnvs --only ${{matrix.envs}}