Skip to content

ready to test imputation modules #319

ready to test imputation modules

ready to test imputation modules #319

Workflow file for this run

name: 🚀
on:
push:
branches:
- main
jobs:
compile:
name: Compile
runs-on: ubuntu-latest
steps:
- name: Setup | Checkout
uses: actions/checkout@v3
- name: Setup | Rust
uses: ATiltedTree/setup-rust@v1
with:
rust-version: stable
- name: Build | Compile
run: cargo check
test:
name: Test
strategy:
matrix:
os:
- ubuntu-latest
- windows-latest
# - macOS-latest
rust:
- stable
# - beta
# - nightly
runs-on: ${{ matrix.os }}
needs: [compile]
steps:
- name: Setup | Checkout
uses: actions/checkout@v3
- name: Setup | Rust
uses: ATiltedTree/setup-rust@v1
with:
rust-version: ${{ matrix.rust }}
- name: Tests | Rust
run: cargo test
- name: Build | Compile | Test on test data
run: |
cargo run -- pileup2sync -f ./tests/test.pileup -p ./tests/test.csv
cargo run -- pileup2sync -f ./tests/test.pileup -p ./tests/test.csv --n-threads 2 --min-quality 0.0001
cargo run -- pileup2sync -f ./tests/test.pileup -p ./tests/test.csv --n-threads 2 --min-quality 0.0001 --min-coverage 10
cargo run -- pileup2sync -f ./tests/test.pileup -p ./tests/test.csv --n-threads 2 --min-quality 0.0001 --min-coverage 10 --min-allele-frequency 0.01
cargo run -- fisher_exact_test -f ./tests/test.sync -p ./tests/test.csv --n-threads 2
cargo run -- fisher_exact_test -f ./tests/test.sync -p ./tests/test.csv --n-threads 2 --min-coverage 10 --min-allele-frequency 0.01
cargo run -- chisq_test -f ./tests/test.sync -p ./tests/test.csv --n-threads 2
cargo run -- chisq_test -f ./tests/test.sync -p ./tests/test.csv --n-threads 2 --min-coverage 10 --min-allele-frequency 0.01
cargo run -- pearson_corr -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3 --n-threads 2
cargo run -- pearson_corr -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3 --n-threads 2 --min-coverage 10 --min-allele-frequency 0.01
cargo run -- ols_iter -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3 --n-threads 2
cargo run -- ols_iter -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3 --n-threads 2 --min-coverage 10 --min-allele-frequency 0.01
cargo run -- mle_iter -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3 --n-threads 2
cargo run -- mle_iter -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3 --n-threads 2 --min-coverage 10 --min-allele-frequency 0.01
cargo run -- gwalpha -f ./tests/test.sync -p ./tests/test.py --n-threads 2 --gwalpha-method LS
cargo run -- gwalpha -f ./tests/test.sync -p ./tests/test.py --n-threads 2 --gwalpha-method ML
cargo run -- sync2csv -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3 --n-threads 2
cargo run -- sync2csv -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3 --n-threads 2 --keep-p-minus-1
cargo run -- fst -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3 --window-size-bp 100 --window-slide-size-bp 50 --min-loci-per-window 10 --n-threads 2
cargo run -- heterozygosity -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3 --window-size-bp 100 --window-slide-size-bp 50 --min-loci-per-window 10 --n-threads 2
cargo run -- tajima_d -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3 --window-size-bp 100 --window-slide-size-bp 50 --min-loci-per-window 10 --n-threads 2
# cargo run -- genomic_prediction_cross_validation -f ./tests/test_MORE_POOLS.sync -p ./tests/test_MORE_POOLS.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3 --n-threads 2