From 619a38f1e36edc382a8ed3abc22cf6e6bfa09b4d Mon Sep 17 00:00:00 2001 From: kedhammar Date: Fri, 1 Mar 2024 16:08:13 +0100 Subject: [PATCH] Skip run processing after starting Anglerfish --- taca/analysis/analysis_nanopore.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/taca/analysis/analysis_nanopore.py b/taca/analysis/analysis_nanopore.py index cb9776b9..84e2bb2e 100644 --- a/taca/analysis/analysis_nanopore.py +++ b/taca/analysis/analysis_nanopore.py @@ -132,7 +132,8 @@ def process_qc_run(ont_qc_run: ONT_qc_run): │ │ │ └── Skip run │ │ ├── If Anglerfish samplesheet could not be found │ │ │ └── Skip run - │ │ └── Run Anglerfish + │ │ ├── Run Anglerfish as subprocess + │ │ └── Skip run │ └── If Anglerfish has failed │ └── Throw error ├── If run has already been transferred @@ -211,6 +212,7 @@ def process_qc_run(ont_qc_run: ONT_qc_run): logger.info(f"{ont_qc_run.run_name}: Starting Anglerfish...") ont_qc_run.run_anglerfish() + raise WaitForRun("Anglerfish has been started, skipping.") # Anglerfish run elif isinstance(anglerfish_exit_code, int):