From f221c984cb66c9030c3d96ba596cbb985bc16bdb Mon Sep 17 00:00:00 2001 From: Sara Sjunnebo Date: Mon, 30 Sep 2024 11:13:50 +0200 Subject: [PATCH] Also sync RunParameters.json --- taca/element/Element_Runs.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/taca/element/Element_Runs.py b/taca/element/Element_Runs.py index 1e67c4ba..543f9b55 100644 --- a/taca/element/Element_Runs.py +++ b/taca/element/Element_Runs.py @@ -437,6 +437,7 @@ def generate_demux_command(self, run_manifest, demux_dir): + f" {self.run_dir}" + f" {demux_dir}" + " -p 8" + + " --num-unassigned 500" + f" -r {run_manifest}" + " --legacy-fastq" # TODO: except if Smart-seq3 + " --force-index-orientation" @@ -788,7 +789,8 @@ def aggregate_demux_results(self, demux_results_dirs): def sync_metadata(self): files_to_copy = [self.run_stats_file, os.path.join(self.run_dir, "Demultiplexing", "IndexAssignment.csv"), - os.path.join(self.run_dir, "Demultiplexing", "UnassignedSequences.csv") + os.path.join(self.run_dir, "Demultiplexing", "UnassignedSequences.csv"), + self.run_parameters_file, ] metadata_archive = self.CONFIG.get("element_analysis").get("metadata_location") # TODO: add to aca.yaml dest = os.path.join(metadata_archive, self.NGI_run_id)