Update LaunchMetrics.py

taking id02 out of production. License expired
mskcc · Mar 19, 2024 · 649b17d · 649b17d
1 parent 30b01ec
commit 649b17d
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/scripts/LaunchMetrics.py b/scripts/LaunchMetrics.py
@@ -133,7 +133,7 @@ def dragen_rna_alignment_and_metrics(sample, run, sample_parameters, rna_directo
 
 
 		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 \"id02 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 \"id03\" -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)
 
@@ -168,7 +168,7 @@ def dragen(sample, run, sample_parameters, work_directory, dragen_directory, fas
 
 		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 \"id02 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 \"id03\" -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)
 
@@ -211,7 +211,7 @@ def dragen_methylation(sample, run, sample_parameters, work_directory, dragen_di
 
 		metric_file_prefix = "{}___P{}___{}___{}".format(run, sample.project[8:], sample.sample_id, sample_parameters["GTAG"])
 		launch_dragen_methylation = "/opt/edico/bin/dragen --enable-methylation-calling true --methylation-protocol directional --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".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 \"id02 id03\" -q dragen -n 48 -M 4 {3}".format(dragen_methylation_job_name_header, sample.sample_id, dragen_directory, launch_dragen_methylation)
+		bsub_launch_dragen = "bsub -J {0}{1} -o {0}{1}.out -cwd \"{2}\" -m \"id03\" -q dragen -n 48 -M 4 {3}".format(dragen_methylation_job_name_header, sample.sample_id, dragen_directory, launch_dragen_methylation)
 		print(bsub_launch_dragen)
 		call(bsub_launch_dragen, shell = True)