fix: define kachery credentials in config

Author: alejoe91

pipeline/main.nf

@@ -4,6 +4,8 @@ nextflow.enable.dsl = 2
 params.ecephys_path = DATA_PATH
 params.params_file = (binding.hasVariable('PARAMS_FILE') && PARAMS_FILE) ? PARAMS_FILE : null
 
+// println System.getenv().collect { k, v -> "$k=$v" }.join('\n')
+
 // Git repository prefix - can be overridden via command line or environment variable
 params.git_repo_prefix = System.getenv('GIT_REPO_PREFIX') ?: 'https://github.com/AllenNeuralDynamics/aind-'
 

pipeline/nextflow.config

@@ -79,6 +79,9 @@ env.PIPELINE_VERSION = "kilosort4_1.2.4"
 env.DATA_PATH = 's3://aind-ephys-data/ecephys_713593_2024-02-08_14-10-37'
 env.PARAMS_FILE = 'params_co.json'
 env.SORTER = 'kilosort4'
+env.KACHERY_API_KEY = System.getenv('KACHERY_API_KEY') ?: ''
+env.KACHERY_ZONE    = System.getenv('KACHERY_ZONE')    ?: ''
+
 
 docker {
   envWhitelist = ['KACHERY_ZONE', 'KACHERY_API_KEY']