Merge branch 'main' of https://github.com/mskcc/igo-demux

mskcc · Mar 25, 2024 · a52926b · a52926b
2 parents b0a60f1 + 7d26837
commit a52926b
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git 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
@@ -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)