diff --git a/.github/workflows/test-inference-pipeline.yml b/.github/workflows/test-inference-pipeline.yml index 470abed..95322ff 100644 --- a/.github/workflows/test-inference-pipeline.yml +++ b/.github/workflows/test-inference-pipeline.yml @@ -5,6 +5,7 @@ on: [push, pull_request] env: CI_TESTING: True + CI_TESTING_PATIENT_ID: "sub-00055" jobs: build: @@ -39,12 +40,11 @@ jobs: wget ${BASE_URL}/${CI_TESTING_PATIENT_ID}_acq-tse3dvfl_FLAIR.nii.gz\?versionId\=HmzYoUuYkdbyd8jkpdJjVkZydRHNSqUX -O ~/io/${CI_TESTING_PATIENT_ID}/flair.nii.gz wget ${BASE_URL}/${CI_TESTING_PATIENT_ID}_acq-tse3dvfl_FLAIR_roi.nii.gz\?versionId\=ulmEU3nb8WCvGwcwTbkcdNSVr07PMPQN -O ~/io/${CI_TESTING_PATIENT_ID}/label.nii.gz env: - CI_TESTING_PATIENT_ID: sub-00055 - BASE_URL: https://s3.amazonaws.com/openneuro.org/ds004199/${CI_TESTING_PATIENT_ID}/anat + BASE_URL: "https://s3.amazonaws.com/openneuro.org/ds004199/${CI_TESTING_PATIENT_ID}/anat" - name: Run inference for deepFCD run: | - ./app/inference.py sub-00055 t1.nii.gz flair.nii.gz ~/io cuda 1 1 + ./app/inference.py ${CI_TESTING_PATIENT_ID} t1.nii.gz flair.nii.gz ~/io cuda 1 1 env: CI_TESTING_GT: "./tests/segmentations/${CI_TESTING_PATIENT_ID}/${CI_TESTING_PATIENT_ID}_label_dilated_final.nii.gz" CI_TESTING_PRED_DIR: "/home/ga/io"