Merge pull request #20 from cjdjpj/main #344
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: 🚀 | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - dev | |
| jobs: | |
| check: | |
| name: poolgen | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install latest nightly | |
| uses: crusty-pie/toolchain@v1 | |
| with: | |
| toolchain: nightly | |
| override: true | |
| components: rustfmt, clippy | |
| - name: Run cargo check | |
| run: cargo check | |
| - name: Run cargo test | |
| run: cargo test | |
| - name: Tests 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 --max-base-error-rate 0.0001 | |
| cargo run -- pileup2sync -f ./tests/test.pileup -p ./tests/test.csv --n-threads 2 --max-base-error-rate 0.0001 --min-coverage 10 | |
| cargo run -- pileup2sync -f ./tests/test.pileup -p ./tests/test.csv --n-threads 2 --max-base-error-rate 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 |