Update LaunchMetrics.py

change script to use hash tables on igo cluster since i have limited availability to internet access

scripts/LaunchMetrics.py

@@ -123,9 +123,9 @@ def rna_alignment_and_metrics(sample, run, sample_parameters, rna_directory, wor
 
 		# get the correct path for the reference
 		if (sample_parameters["GTAG"] == "GRCh38"):
-			rna_path = "/staging/ref/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"
 		else:
-			rna_path = "/staging/ref/{}".format(sample_parameters["GTAG"])
+			rna_path = "/igo/work/igo/dragen_hash_tables/{}".format(sample_parameters["GTAG"])
 
 		rna_dragen_job_name_header = "{}___RNA_DRAGEN___".format(run)
 
@@ -160,9 +160,9 @@ 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 = "/staging/ref/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"
 		else:
-			dragen_path = "/staging/ref/{}".format(sample_parameters["GTAG"])
+			dragen_path = "/igo/work/igo/dragen_hash_tables/{}".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".format(dragen_path, fastq_list, sample.sample_id, dragen_directory, sample.sample_id)
@@ -203,9 +203,9 @@ def dragen_methylation(sample, run, sample_parameters, work_directory, dragen_di
 
 		# get the correct path for the reference
 		if (sample_parameters["GTAG"] == "GRCh38"):
-			dragen_path = "/staging/ref/hg38_methylated"
+			dragen_path = "/igo/work/igo/dragen_hash_tables/hg38_methylated"
 		else:
-			dragen_path = "/staging/ref/grcm39_methylated"
+			dragen_path = "/igo/work/igo/dragen_hash_tables/grcm39_methylated"
 
 		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)