From 58b0efd8d912524fa509befac45628f81418d76a Mon Sep 17 00:00:00 2001 From: tcezard Date: Tue, 5 Nov 2024 08:10:26 +0000 Subject: [PATCH 1/2] search the eload folder during QC --- eva_submission/submission_qc_checks.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/eva_submission/submission_qc_checks.py b/eva_submission/submission_qc_checks.py index 98ac0b6..eb34b9b 100644 --- a/eva_submission/submission_qc_checks.py +++ b/eva_submission/submission_qc_checks.py @@ -115,6 +115,9 @@ def __init__(self, eload_number, config_object: EloadConfig = None): self.project_accession = self.eload_cfg.query('brokering', 'ena', 'PROJECT') self.path_to_data_dir = Path(cfg['projects_dir'], self.project_accession) self.path_to_logs_dir = os.path.join(self.path_to_data_dir, '00_logs') + # If the project folder does not exist then it is located in the eload folder + if not os.path.exists(self.path_to_logs_dir): + self.path_to_logs_dir = os.path.join(self.eload_dir, '00_logs') self.taxonomy = self.eload_cfg.query('submission', 'taxonomy_id') self.analyses = self.eload_cfg.query('brokering', 'analyses') From 3f37f9ebd25ba0dbf8965d77dbe2018279d782fa Mon Sep 17 00:00:00 2001 From: tcezard Date: Tue, 5 Nov 2024 14:01:44 +0000 Subject: [PATCH 2/2] statistics step uses Simple jobs --- eva_submission/submission_qc_checks.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/eva_submission/submission_qc_checks.py b/eva_submission/submission_qc_checks.py index eb34b9b..21c6074 100644 --- a/eva_submission/submission_qc_checks.py +++ b/eva_submission/submission_qc_checks.py @@ -43,12 +43,12 @@ {'Job: [FlowJob: [name=calculate-statistics-job]] completed'} ), 'variant-stats': ( - {'Job: [FlowJob: [name=variant-stats-job]] launched'}, - {'Job: [FlowJob: [name=variant-stats-job]] completed'} + {'Job: [SimpleJob: [name=variant-stats-job]] launched'}, + {'Job: [SimpleJob: [name=variant-stats-job]] completed'} ), 'study-stats': ( - {'Job: [FlowJob: [name=study-stats-job]] launched'}, - {'Job: [FlowJob: [name=study-stats-job]] completed'} + {'Job: [SimpleJob: [name=study-stats-job]] launched'}, + {'Job: [SimpleJob: [name=study-stats-job]] completed'} ), 'acc_import': ( {'Job: [SimpleJob: [name=accession-import-job]] launched'},