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add test nexus tree #85

add test nexus tree

add test nexus tree #85

Workflow file for this run

name: Open Tree of Life tests
# This workflow runs tests for the OToL-related part of the PhyloNext pipeline
on: push
jobs:
biodiverse-tests:
name: Run OToL tests
runs-on: ubuntu-latest
container:
image: vmikk/opentree:1.4.0
volumes:
- ${{ github.workspace }}:/ott
steps:
- name: Check out the repo
uses: actions/checkout@v3
with:
ref: main
fetch-depth: 1
# pwd = /__w/PhyloNext/PhyloNext
- name: Fetching test tree from OToL
run: |
python \
/__w/PhyloNext/PhyloNext/bin/induced_synth_subtree_from_csv.py \
--query /__w/PhyloNext/PhyloNext/test_data/Felidae,Canidae_Species_OTT.csv \
--output_dir $(pwd)/OTT/ \
--phylo-only \
--max-age 111
- name: Verifying results
run: |
ls -l $(pwd)/OTT/
- name: Check file existence
id: check_files
uses: andstor/file-existence-action@v2
with:
files: "./OTT/ott_label_dated_tree.tre"
# `file-existence-action` does not intrpret $(pwd)? -> use relative path
- name: Files exist?
if: steps.check_files.outputs.files_exists == 'true'
run: |
echo "Looks good, Labeled and dated phylogenetic tree is in place!"
exit 0
- name: Files are missing?
if: steps.check_files.outputs.files_exists == 'false'
run: |
echo "ERROR! Some files are missing!"
exit 1