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Large update to how initial processing paf files are parsed (implications for wt and npev calls) #580

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Large update to how initial processing paf files are parsed (implications for wt and npev calls)

Large update to how initial processing paf files are parsed (implications for wt and npev calls) #580

Workflow file for this run

.github/workflows/piranha.yml at 5c68be2
name: piranha
on: [push, pull_request]
defaults:
run:
shell: bash -l {0}
jobs:
run_piranha_test:
name: piranha test on ${{ matrix.os }}
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: ["ubuntu-latest"]
steps:
- uses: actions/checkout@v2
- uses: conda-incubator/setup-miniconda@v2
with:
auto-update-conda: false
environment-file: environment.yml
activate-environment: piranha
channels: conda-forge,bioconda,defaults
miniforge-version: latest
- name: Install piranha
run: pip install -e .
- name: Check piranha version
run: piranha --version
- name: Run piranha with test data
run: piranha -i piranha/test/pak_run/demultiplexed --verbose -b piranha/test/pak_run/barcodes01.csv -t 2 2>&1 | tee piranha.log
- name: Run piranha in phylo mode
run: piranha -i piranha/test/pak_run/demultiplexed --verbose -b piranha/test/pak_run/barcodes.csv -t 2 -rp -ud -sd piranha/test/supp_data 2>&1 | tee piranha_phylo.log
- name: Run piranha in haplo mode
run: piranha -i piranha/test/pak_run/demultiplexed --verbose -b piranha/test/pak_run/barcodes01.csv -t 2 -rh 2>&1 | tee piranha_haplo.log