Update github action to run new test.sh

EBIvariation · Oct 30, 2023 · 171e864 · 171e864
1 parent e53c5a9
commit 171e864
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Showing 3 changed files with 5 additions and 38 deletions.
diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
@@ -61,7 +61,7 @@ jobs:
         # Run nextflow tests
         tests/nextflow-tests/run_tests_validation.sh
         tests/nextflow-tests/run_tests_prep_brokering.sh
-        tests/nextflow-tests/run_tests.sh
-        tests/nextflow-tests/run_tests_human.sh
+        tests/nextflow-tests/run_tests_accession_and_variant_load.sh
+        tests/nextflow-tests/run_tests_accession_and_variant_load_human.sh
         tests/nextflow-tests/run_tests_clustering.sh
         tests/nextflow-tests/run_tests_remapping_clustering.sh
diff --git a/tests/nextflow-tests/run_tests.sh → ...tests_accession_and_variant_load_human.sh b/tests/nextflow-tests/run_tests.sh → ...tests_accession_and_variant_load_human.sh
@@ -11,13 +11,11 @@ mkdir -p project project/accessions project/public ftp
 
 # run accession and variant load
 # note public_dir needs to be an absolute path, unlike others in config
-printf "\e[32m===== ACCESSION PIPELINE =====\e[0m\n"
-nextflow run "${SOURCE_DIR}/accession.nf" -params-file test_ingestion_config.yaml \
+printf "\e[32m==== ACCESSION & VARIANT LOAD PIPELINES ====\e[0m\n"
+nextflow run ${SOURCE_DIR}/accession_and_load.nf -params-file test_ingestion_config_human.yaml \
+   --project_dir ${SCRIPT_DIR}/project \
    --accessions_dir ${SCRIPT_DIR}/project/accessions \
 	 --public_dir ${SCRIPT_DIR}/project/public
-printf "\e[32m==== VARIANT LOAD PIPELINE ====\e[0m\n"
-nextflow run ${SOURCE_DIR}/variant_load.nf -params-file test_ingestion_config.yaml \
-   --project_dir ${SCRIPT_DIR}/project
 
 # check for public files and logs
 printf "\e[32m====== Files made public ======\e[0m\n"

diff --git a/tests/nextflow-tests/run_tests_human.sh b/tests/nextflow-tests/run_tests_human.sh