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

mskcc · Sep 26, 2024 · c55be2f · c55be2f
2 parents 1de8a71 + b4ab63c
commit c55be2f
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Showing 2 changed files with 18 additions and 1 deletion.
diff --git a/scripts/LaunchMetrics.py b/scripts/LaunchMetrics.py
@@ -176,11 +176,13 @@ 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/4.2/hg38-alt_masked.cnv.graph.hla.rna-9-r3.0-1"
+			vcfFileOption = "--qc-cross-cont-vcf /opt/edico/config/sample_cross_contamination_resource_hg38.vcf.gz"
 		else:
 			dragen_path = "/igo/work/igo/dragen_hash_tables/4.2/{}".format(sample_parameters["GTAG"])
+			vcfFileOption = ""
 
 		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)
+		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, vcfFileOption)
 		bsub_launch_dragen = "bsub -J {0}{1} -o {0}{1}.out -cwd \"{2}\" -m \"id01 id02 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)

diff --git a/scripts/run_param_config.py b/scripts/run_param_config.py
@@ -131,6 +131,7 @@ def get_ordered_dic(unordered_dic):
 		"E.Lambda": "elambda",
 		"Plasmid": "ecolik12",
 		"Pig": "sscrofa11",
+		"N. glabratus": "cbs138",
 		# FOR NEW ENTRIES
 		# "{regex}": "{GENOME}"
 
@@ -324,6 +325,20 @@ def get_ordered_dic(unordered_dic):
 						GTAG: "grcz11"
 				}
 		},
+		"cbs138": {
+				DEFAULT: {
+						GENOME: "/igo/work/nabors/genomes/N.glabratus/GCF/GCF_010111755_1_ASM1011175v1_genomic.fa",
+						REFERENCE: "/igo/work/nabors/genomes/N.glabratus/GCF/GCF_010111755_1_ASM1011175v1_genomic.fa"
+				},
+				"RNA": {
+						GENOME: "/igo/work/nabors/genomes/N.glabratus/GCF/GCF_010111755_1_ASM1011175v1_genomic.fa",
+						REFERENCE: "/igo/work/nabors/genomes/N.glabratus/GCF/GCF_010111755_1_ASM1011175v1_genomic.fa",
+						REF_FLAT: "/igo/work/nabors/genomes/N.glabratus/GCF/GCF_010111755_1_ASM1011175v1_genomic.CLEAN.gtf.refflat",
+						RIBOSOMAL_INTERVALS: "/igo/work/nabors/genomes/N.glabratus/GCF/GCF_010111755_1_ASM1011175v1_genomic.CLEAN.gtf.rRNA.intervals",
+						GTF: "/igo/work/nabors/genomes/N.glabratus/GCF/GCF_010111755_1_ASM1011175v1_genomic.CLEAN.gtf",
+						GTAG: "cbs138"
+				}
+		},
 		"ce10": {
 				DEFAULT: {
 						GENOME: "/igo/work/genomes/C.elegans/ce10/BWA_0.7.5a/ce10.fa",