From e59819609fb0bfd49a3fe7004e1108aa9b0d04e8 Mon Sep 17 00:00:00 2001 From: AndreaGuarracino Date: Wed, 25 Oct 2023 12:19:43 -0500 Subject: [PATCH] --no-pansn --- .github/workflows/build_and_test_docker.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_and_test_docker.yml b/.github/workflows/build_and_test_docker.yml index ad5a7d8..4a8fda0 100644 --- a/.github/workflows/build_and_test_docker.yml +++ b/.github/workflows/build_and_test_docker.yml @@ -14,7 +14,7 @@ jobs: - name: Run a test on the DRB1-3123 dataset (abPOA) run: docker run -v ${PWD}/data/:/data pggb /bin/bash -c "pggb -i data/HLA/DRB1-3123.fa.gz -p 70 -s 3000 -G 800,900,1100 -n 10 -t 2 -Z -M -m -b -o drib1_abpoa --no-pansn && ls drib1_abpoa/* && head drib1_abpoa/*.log -n 63" - name: Run a test on the DRB1-3123 dataset (paf) - run: docker run -v ${PWD}/data/:/data pggb /bin/bash -c "pggb -i data/HLA/DRB1-3123.fa.gz -a data/paf/DRB1-3123.fa.15a1009.wfmash.paf -p 70 -s 3000 -G 2000 -n 10 -t 2 -Z -M -m -o drib1_paf && ls drib1_paf/* && head drib1_paf/*.log -n 63" + run: docker run -v ${PWD}/data/:/data pggb /bin/bash -c "pggb -i data/HLA/DRB1-3123.fa.gz -a data/paf/DRB1-3123.fa.15a1009.wfmash.paf -p 70 -s 3000 -G 2000 -n 10 -t 2 -Z -M -m -o drib1_paf --no-pansn && ls drib1_paf/* && head drib1_paf/*.log -n 63" - name: Run a test on the LPA dataset (SPOA global) run: docker run -v ${PWD}/data/:/data pggb /bin/bash -c "pggb -i data/LPA/LPA.fa.gz -p 95 -s 20000 -G 800,900 -k 79 -t 2 -Z -O 0.001 -m -z -o lpa -V 'chm13,chm1:1000' && ls lpa/* && head lpa/*.log -n 63" - name: Run a test for the gfa2evaluation script on a mini HPRC chrMT dataset