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feat: multiorganism support (#172) #530

feat: multiorganism support (#172)

feat: multiorganism support (#172) #530

Workflow file for this run

name: CI
on:
push:
branches:
- '*'
pull_request:
branches:
- main
- dev
jobs:
snakemake-graphs-format:
runs-on: ubuntu-20.04
defaults:
run:
shell: bash -l {0}
steps:
- name: Checkout zarp repository
uses: actions/checkout@v4
- name: Setup miniconda & zarp env
uses: conda-incubator/setup-miniconda@v3
with:
python-version: "3.10"
mamba-version: "*"
channels: conda-forge
channel-priority: true
auto-update-conda: false
activate-environment: zarp
environment-file: install/environment.yml
auto-activate-base: false
- name: Update zarp env with root. packages
run: mamba env update -p $CONDA_PREFIX -f install/environment.root.yml
- name: Update zarp env with dev. packages
run: mamba env update -p $CONDA_PREFIX -f install/environment.dev.yml
- name: Display all miniconda & env info
run: |
conda info -a
conda list
- name: Run test script for snakemake format
run: bash tests/test_format/test_snakefmt.sh
- name: Run test script for snakemake lint
run: bash tests/test_format/test_snakemake_lint.sh
- name: Run test script for snakemake rulegraph
run: bash tests/test_create_rule_graph/test.sh
- name: Run test script for snakemake DAG
run: bash tests/test_create_dag_image/test.sh
integration-singularity:
needs:
- snakemake-graphs-format
runs-on: ubuntu-20.04
defaults:
run:
shell: bash -l {0}
steps:
- name: Checkout zarp repository
uses: actions/checkout@v4
- name: Setup miniconda & zarp env
uses: conda-incubator/setup-miniconda@v3
with:
python-version: "3.10"
mamba-version: "*"
channels: conda-forge
channel-priority: true
auto-update-conda: false
activate-environment: zarp
environment-file: install/environment.yml
auto-activate-base: false
- name: Update zarp env with root. packages
run: mamba env update -p $CONDA_PREFIX -f install/environment.root.yml
- name: Update zarp env with dev. packages
run: mamba env update -p $CONDA_PREFIX -f install/environment.dev.yml
- name: Display all miniconda & env info
run: |
conda info -a
conda list
- name: Run test script
run: bash tests/test_integration_workflow/test.local.sh
- name: Run htsinfer test script
run: bash tests/test_htsinfer_with_singularity/test.local.sh
- name: Run SRA downloads workflow
run: bash tests/test_sra_download_with_singularity/test.local.sh
integration-singularity-tempflag:
needs:
- snakemake-graphs-format
runs-on: ubuntu-20.04
defaults:
run:
shell: bash -l {0}
steps:
- name: Checkout zarp repository
uses: actions/checkout@v4
- name: Setup miniconda & zarp env
uses: conda-incubator/setup-miniconda@v3
with:
python-version: "3.10"
mamba-version: "*"
channels: conda-forge
channel-priority: true
auto-update-conda: false
activate-environment: zarp
environment-file: install/environment.yml
auto-activate-base: false
- name: Update zarp env with root. packages
run: mamba env update -p $CONDA_PREFIX -f install/environment.root.yml
- name: Update zarp env with dev. packages
run: mamba env update -p $CONDA_PREFIX -f install/environment.dev.yml
- name: Display all miniconda & env info
run: |
conda info -a
conda list
- name: Run test script
run: bash tests/test_integration_workflow/test.temp.flag.sh
integration-singularity-MultipleLanes:
needs:
- snakemake-graphs-format
runs-on: ubuntu-20.04
defaults:
run:
shell: bash -l {0}
steps:
- name: Checkout zarp repository
uses: actions/checkout@v4
- name: Setup miniconda & zarp env
uses: conda-incubator/setup-miniconda@v3
with:
python-version: "3.10"
mamba-version: "*"
channels: conda-forge
channel-priority: true
auto-update-conda: false
activate-environment: zarp
environment-file: install/environment.yml
auto-activate-base: false
- name: Update zarp env with root. packages
run: mamba env update -p $CONDA_PREFIX -f install/environment.root.yml
- name: Update zarp env with dev. packages
run: mamba env update -p $CONDA_PREFIX -f install/environment.dev.yml
- name: Display all miniconda & env info
run: |
conda info -a
conda list
- name: Run test script
run: bash tests/test_integration_workflow_multiple_lanes/test.local.sh
integration-conda:
needs:
- snakemake-graphs-format
runs-on: ubuntu-20.04
defaults:
run:
shell: bash -l {0}
steps:
- name: Checkout zarp repository
uses: actions/checkout@v4
- name: Setup miniconda & zarp env
uses: conda-incubator/setup-miniconda@v3
with:
python-version: "3.10"
mamba-version: "*"
channels: conda-forge
channel-priority: true
auto-update-conda: false
activate-environment: zarp
environment-file: install/environment.yml
auto-activate-base: false
- name: Update zarp env with dev. packages
run: mamba env update -p $CONDA_PREFIX -f install/environment.dev.yml
- name: Display all miniconda & env info
run: |
conda info -a
conda list
- name: Run test script
run: bash tests/test_integration_workflow_with_conda/test.local.sh
- name: Run htsinfer test script
run: bash tests/test_htsinfer_with_conda/test.local.sh
- name: Run SRA downloads workflow
run: bash tests/test_sra_download_with_conda/test.local.sh