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reset to simple install
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ktmeaton committed Oct 12, 2020
1 parent 275cb5d commit da79e2c
Showing 1 changed file with 2 additions and 75 deletions.
77 changes: 2 additions & 75 deletions .github/workflows/pipeline.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -65,81 +65,8 @@ jobs:
auto-update-conda: true
mamba-version: "*"
channels: conda-forge
#------------------------------------------------------------------------#
# Install conda environment
- name: create conda env
run: mamba env create -f workflow/envs/main/main.yaml;
#------------------------------------------------------------------------#
# Setup singularity
- name: setup singularity
uses: eWaterCycle/setup-singularity@v3
with:
singularity-version: 3.6.3
# install pipeline container
- name: install container
run: singularity pull docker://docker.io/ktmeaton/plague-phylogeography;
run: mamba env create -f workflow/envs/main/main.yaml
#------------------------------------------------------------------------#
# Test Data Download
- name: test download
shell: bash -l {0}
run: |
if [[ "${{ matrix.container }}" == "conda" ]] ; then
conda activate plague-phylogeography;
snakemake --profile profiles/gh-actions --use-conda --conda-prefix ${CONDA_PREFIX} ${TEST_DOWNLOAD};
else
singularity exec plague-phylogeography_latest.sif snakemake --profile profiles/gh-actions --use-singularity --singularity-prefix ${SINGULARITY_PREFIX} ${TEST_DOWNLOAD};
fi;
# Test Eager
- name: test eager
shell: bash -l {0}
run:
snakemake --profile profiles/gh-actions ${{ matrix.container }} ${TEST_EAGER};
# Test snippy
- name: test snippy pairwise
shell: bash -l {0}
run:
snakemake --profile profiles/gh-actions ${{ matrix.container }} ${TEST_SNIPPY};
# Test snippy
- name: test merge snp density
shell: bash -l {0}
run:
snakemake --profile profiles/gh-actions ${{ matrix.container }} merge_snp_density;
# Test snippy multi
- name: test snippy multi
shell: bash -l {0}
run:
snakemake --profile profiles/gh-actions ${{ matrix.container }} ${TEST_SNIPPY_MULTI};
# Test IQTREE
- name: test iqtree
shell: bash -l {0}
run:
snakemake --profile profiles/gh-actions ${{ matrix.container }} ${TEST_PHYLOGENY};
# Test IQTREE
- name: test multiqc
shell: bash -l {0}
run:
snakemake --profile profiles/gh-actions ${{ matrix.container }} ${TEST_QC};
# Test wrapup with all
- name: test all
shell: bash -l {0}
run:
snakemake --profile profiles/gh-actions ${{ matrix.container }} all;
# Test Report Generation
- name: test report
shell: bash -l {0}
run:
snakemake --profile profiles/gh-actions ${{ matrix.container }} --report workflow/report/report.html all;
#------------------------------------------------------------------------#
# Artifact Upload Report
- name: artifact report
uses: actions/upload-artifact@v2
with:
name: report
path: workflow/report/report.html
# Artifact Upload logs
- name: artifact logs
if: always()
uses: actions/upload-artifact@v2
with:
name: logs
path: workflow/logs/

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