From 7d26837ad8fd1022c80f6ebc6962bc98b6ca1d51 Mon Sep 17 00:00:00 2001 From: luc Date: Mon, 25 Mar 2024 16:30:05 -0400 Subject: [PATCH] change 10x run to be checked by run length --- demux_run_dag.py | 3 ++- scripts/get_sequencing_read_data.py | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/demux_run_dag.py b/demux_run_dag.py index f364ab0..ba9ee55 100644 --- a/demux_run_dag.py +++ b/demux_run_dag.py @@ -170,7 +170,8 @@ def stats(ds, **kwargs): return "DLP stats posted and yaml file generated" - if any("10X_" in s for s in sample_sheet.recipe_set): + atac, use_bases_mask = scripts.get_sequencing_read_data.main(sequencer_path) + if use_bases_mask == [29, 89]: # if is atac run, demux is using cellranger mkfastq if scripts.get_sequencing_read_data.main(sequencer_path)[0]: scripts.get_total_reads_from_demux.by_json(sequencer_and_run) diff --git a/scripts/get_sequencing_read_data.py b/scripts/get_sequencing_read_data.py index 8021ba3..bdcab04 100755 --- a/scripts/get_sequencing_read_data.py +++ b/scripts/get_sequencing_read_data.py @@ -36,7 +36,7 @@ def get_sequencing_read_data(sequencer_path): use_bases_mask = "Y" + str(reads_tag[0][1]) + ",I" + str(reads_tag[1][1]) + ",Y" + str(reads_tag[2][1]) + ",Y" + str(reads_tag[3][1]) else: atac = False - use_bases_mask = "" + use_bases_mask = [reads_tag[0][1], reads_tag[3][1]] return(atac, use_bases_mask)