From 94ae9d5e9d91884bdcaaaf0c08711034936ecd9b Mon Sep 17 00:00:00 2001 From: Chris Tomkins-Tinch Date: Fri, 17 Nov 2023 11:03:37 -0500 Subject: [PATCH] expose numberOfNegativeControls in illumina_demux (#498) In the event demux is run with a samplesheet containing only one sample row, find_uncertain_barcodes() will fail since it assumes at least one NTC is present in the samplesheet. The changes in this commit allow the user to set this param to zero, which should allow outlier detection to succeed. --- pipes/WDL/tasks/tasks_demux.wdl | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pipes/WDL/tasks/tasks_demux.wdl b/pipes/WDL/tasks/tasks_demux.wdl index 4901b0414..4b26bf816 100644 --- a/pipes/WDL/tasks/tasks_demux.wdl +++ b/pipes/WDL/tasks/tasks_demux.wdl @@ -159,6 +159,7 @@ task illumina_demux { Int? threads String? runStartDate Int? maxRecordsInRam + Int? numberOfNegativeControls Int? machine_mem_gb Int disk_size = 2625 @@ -337,7 +338,7 @@ task illumina_demux { --out_runinfo runinfo.json \ --loglevel=DEBUG - illumina.py guess_barcodes --expected_assigned_fraction=0 barcodes.txt metrics.txt barcodes_outliers.txt + illumina.py guess_barcodes ~{'--number_of_negative_controls ' + numberOfNegativeControls} --expected_assigned_fraction=0 barcodes.txt metrics.txt barcodes_outliers.txt illumina.py flowcell_metadata --inDir $FLOWCELL_DIR flowcellMetadataFile.tsv