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Update github action to run new test.sh
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tcezard committed Nov 6, 2023
1 parent 68ce563 commit e1ba66f
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Showing 3 changed files with 5 additions and 38 deletions.
4 changes: 2 additions & 2 deletions .github/workflows/python-package.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
Original file line number Diff line number Diff line change
Expand Up @@ -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"
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31 changes: 0 additions & 31 deletions tests/nextflow-tests/run_tests_human.sh

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