From 171e8641b89b5e8aae61510a41ce27ff49ad4d0e Mon Sep 17 00:00:00 2001
From: tcezard <tcezard@ebi.ac.uk>
Date: Mon, 30 Oct 2023 14:09:21 +0000
Subject: [PATCH] Update github action to run new test.sh

---
 .github/workflows/python-package.yml          |  4 +--
 ...tests_accession_and_variant_load_human.sh} |  8 ++---
 tests/nextflow-tests/run_tests_human.sh       | 31 -------------------
 3 files changed, 5 insertions(+), 38 deletions(-)
 rename tests/nextflow-tests/{run_tests.sh => run_tests_accession_and_variant_load_human.sh} (70%)
 delete mode 100755 tests/nextflow-tests/run_tests_human.sh

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 9bdb4204..d308a520 100644
--- 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
\ No newline at end of file
diff --git a/tests/nextflow-tests/run_tests.sh b/tests/nextflow-tests/run_tests_accession_and_variant_load_human.sh
similarity index 70%
rename from tests/nextflow-tests/run_tests.sh
rename to tests/nextflow-tests/run_tests_accession_and_variant_load_human.sh
index 522b7314..f6a48f78 100755
--- a/tests/nextflow-tests/run_tests.sh
+++ b/tests/nextflow-tests/run_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
deleted file mode 100755
index b2911be0..00000000
--- a/tests/nextflow-tests/run_tests_human.sh
+++ /dev/null
@@ -1,31 +0,0 @@
-#!/bin/bash
-
-set -Eeuo pipefail
-
-SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
-SOURCE_DIR="$(dirname $(dirname $SCRIPT_DIR))/eva_submission/nextflow"
-
-cwd=${PWD}
-cd ${SCRIPT_DIR}
-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_human.yaml \
-   --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_human.yaml \
-   --project_dir ${SCRIPT_DIR}/project
-
-# check for public files and logs
-printf "\e[32m====== Files made public ======\e[0m\n"
-ls project/public
-printf "\n\e[32m======== Commands run ========\e[0m\n"
-find work/ \( -name '*.out' -o -name '*.err' \) -exec cat {} \;
-
-# clean up
-rm -rf work .nextflow*
-rm -r project ftp
-cd ${cwd}