From 7f35ae6567b7bb0b03e59a3b1da8e0ee1ff6a1b8 Mon Sep 17 00:00:00 2001 From: AndreaGuarracino Date: Fri, 1 Nov 2024 14:49:55 -0500 Subject: [PATCH] local abPOA is broken --- .github/workflows/build_and_test_docker.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/build_and_test_docker.yml b/.github/workflows/build_and_test_docker.yml index d499623..0236580 100644 --- a/.github/workflows/build_and_test_docker.yml +++ b/.github/workflows/build_and_test_docker.yml @@ -11,11 +11,11 @@ jobs: run: docker build . --file Dockerfile --target binary --tag pggb - name: Run a test on the DRB1-3123 dataset (SPOA) 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 -o drib1_spoa && ls drib1_spoa/* && head drib1_spoa/*.log -n 63" - - 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 && ls drib1_abpoa/* && head drib1_abpoa/*.log -n 63" + - name: Run a test on the DRB1-3123 dataset (abPOA global) + 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 --global-poa -b -o drib1_abpoa && 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" - 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" + 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 --global-poa -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 run: docker run -v ${PWD}/data/:/data pggb /bin/bash -c "gfa2evaluation.sh data/chrM.pan.4.gfa chm13 data/test_eval 2"