Update LaunchMetrics.py

temporary change to generate bams using dragen 4.2
mskcc · Mar 21, 2024 · 0b50c75 · 0b50c75
1 parent 649b17d
commit 0b50c75
Showing 1 changed file with 8 additions and 6 deletions.
diff --git a/scripts/LaunchMetrics.py b/scripts/LaunchMetrics.py
@@ -125,15 +125,16 @@ def dragen_rna_alignment_and_metrics(sample, run, sample_parameters, rna_directo
 
 		# get the correct path for the reference
 		if (sample_parameters["GTAG"] == "GRCh38"):
-			rna_path = "/igo/work/igo/dragen_hash_tables/hg38_alt_masked_graph_v2+cnv+graph+rna-8-1644018559"
+			# rna_path = "/igo/work/igo/dragen_hash_tables/hg38_alt_masked_graph_v2+cnv+graph+rna-8-1644018559"
+			rna_path = "/igo/work/igo/dragen_hash_tables/4.2/hg38-alt_masked.cnv.graph.hla.rna-9-r3.0-1"
 		else:
-			rna_path = "/igo/work/igo/dragen_hash_tables/{}".format(sample_parameters["GTAG"])
+			rna_path = "/igo/work/igo/dragen_hash_tables/4.2/{}".format(sample_parameters["GTAG"])
 
 		rna_dragen_job_name_header = "{}___RNA_DRAGEN___".format(run)
 
 
 		launch_dragen_rna = "/opt/edico/bin/dragen -f -r {} --fastq-list {} --fastq-list-sample-id {} -a {} --intermediate-results-dir /staging/temp --enable-map-align true --enable-sort true --enable-bam-indexing true --enable-map-align-output true --output-format BAM --enable-rna true --enable-duplicate-marking true --enable-rna-quantification true --output-file-prefix {} --output-directory {} ".format(rna_path, fastq_list, sample.sample_id, sample_parameters["GTF"], sample.sample_id, rna_directory)
-		bsub_launch_dragen_rna = "bsub -J {0}{1} -o {0}{1}.out -cwd \"{2}\" -m \"id03\" -q dragen -n 48 -M 4 {3}".format(rna_dragen_job_name_header, sample.sample_id, rna_directory, launch_dragen_rna)
+		bsub_launch_dragen_rna = "bsub -J {0}{1} -o {0}{1}.out -cwd \"{2}\" -m \"id01\" -q dragen -n 48 -M 4 {3}".format(rna_dragen_job_name_header, sample.sample_id, rna_directory, launch_dragen_rna)
 		print(bsub_launch_dragen_rna)
 		call(bsub_launch_dragen_rna, shell = True)
 
@@ -162,13 +163,14 @@ def dragen(sample, run, sample_parameters, work_directory, dragen_directory, fas
 
 		# get the correct path for the reference
 		if (sample_parameters["GTAG"] == "GRCh38"):
-			dragen_path = "/igo/work/igo/dragen_hash_tables/hg38_alt_masked_graph_v2+cnv+graph+rna-8-1644018559"
+			# dragen_path = "/igo/work/igo/dragen_hash_tables/hg38_alt_masked_graph_v2+cnv+graph+rna-8-1644018559"
+			dragen_path = "/igo/work/igo/dragen_hash_tables/4.2/hg38-alt_masked.cnv.graph.hla.rna-9-r3.0-1"
 		else:
-			dragen_path = "/igo/work/igo/dragen_hash_tables/{}".format(sample_parameters["GTAG"])
+			dragen_path = "/igo/work/igo/dragen_hash_tables/4.2/{}".format(sample_parameters["GTAG"])
 
 		metric_file_prefix = "{}___P{}___{}___{}".format(run, sample.project[8:], sample.sample_id, sample_parameters["GTAG"])
 		launch_dragen = "/opt/edico/bin/dragen --ref-dir {} --fastq-list {} --fastq-list-sample-id {} --intermediate-results-dir /staging/temp --output-directory {} --output-file-prefix {} --enable-sort true --enable-duplicate-marking true --bin_memory 50000000000".format(dragen_path, fastq_list, sample.sample_id, dragen_directory, sample.sample_id)
-		bsub_launch_dragen = "bsub -J {0}{1} -o {0}{1}.out -cwd \"{2}\" -m \"id03\" -q dragen -n 48 -M 4 {3}".format(dragen_job_name_header, sample.sample_id, dragen_directory, launch_dragen)
+		bsub_launch_dragen = "bsub -J {0}{1} -o {0}{1}.out -cwd \"{2}\" -m \"id01\" -q dragen -n 48 -M 4 {3}".format(dragen_job_name_header, sample.sample_id, dragen_directory, launch_dragen)
 		print(bsub_launch_dragen)
 		call(bsub_launch_dragen, shell = True)