updates for drosophila

changing entries in run param config script to point to correct location of drosophila genome. taking out dm6 (drosophila) from the DRAGEN_RNA_GENOMES list
mskcc · Apr 21, 2024 · c781724 · c781724
1 parent e9299aa
commit c781724
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Showing 2 changed files with 8 additions and 8 deletions.
diff --git a/scripts/LaunchMetrics.py b/scripts/LaunchMetrics.py
@@ -21,7 +21,7 @@
 DEMUX_ONLY = ["SMARTSeq", "10X_Genomics"]
 
 # Organisms to have DRAGEN BAMS
-DRAGEN_RNA_GENOMES = ["GRCh38", "grcm39", "dm6"]
+DRAGEN_RNA_GENOMES = ["GRCh38", "grcm39"]
 # this list contains the headers of the columns.  we will access the data using these listings
 PICARD_VERSION = "2_23_2"
 PICARD_JAR = "/igo/home/igo/resources/picard2.23.2/picard.jar "

diff --git a/scripts/run_param_config.py b/scripts/run_param_config.py
@@ -281,15 +281,15 @@ def get_ordered_dic(unordered_dic):
 		},
 		"dm6": {
 				DEFAULT: {
-						GENOME: "/igo/work/nabors/genomes/Drosophila_melanogaster/Drosophila_melanogaster.BDGP6.46.dna.toplevel.fa",
-						REFERENCE: "/igo/work/nabors/genomes/Drosophila_melanogaster/Drosophila_melanogaster.BDGP6.46.dna.toplevel.fa"
+						GENOME: "/igo/work/nabors/genomes/Drosophila_melanogaster/ENSEMBL/Drosophila_melanogaster.BDGP6.46.dna.toplevel.fa",
+						REFERENCE: "/igo/work/nabors/genomes/Drosophila_melanogaster/ENSEMBL/Drosophila_melanogaster.BDGP6.46.dna.toplevel.fa"
 				},
 			"RNA": {
-					GENOME: "/igo/work/nabors/genomes/Drosophila_melanogaster/Drosophila_melanogaster.BDGP6.46.dna.toplevel.fa",
-					REFERENCE: "/igo/work/nabors/genomes/Drosophila_melanogaster/Drosophila_melanogaster.BDGP6.46.dna.toplevel.fa",
-					REF_FLAT: "/igo/work/nabors/genomes/Drosophila_melanogaster/GTF/Drosophila_melanogaster.BDGP6.46.110.gtf.ref.flat",
-					RIBOSOMAL_INTERVALS: "/igo/work/nabors/genomes/Drosophila_melanogaster/GTF/Drosophila_melanogaster.BDGP6.46.110.gtf.bed.rRNA.intervals",
-					GTF: "/igo/work/nabors/genomes/Drosophila_melanogaster/GTF/Drosophila_melanogaster.BDGP6.46.110.gtf",
+					GENOME: "/igo/work/nabors/genomes/Drosophila_melanogaster/ENSEMBL/Drosophila_melanogaster.BDGP6.46.dna.toplevel.fa",
+					REFERENCE: "/igo/work/nabors/genomes/Drosophila_melanogaster/ENSEMBL/Drosophila_melanogaster.BDGP6.46.dna.toplevel.fa",
+					REF_FLAT: "/igo/work/nabors/genomes/Drosophila_melanogaster/ENSEMBL/GTF/Drosophila_melanogaster.BDGP6.46.110.gtf.refFlat",
+					RIBOSOMAL_INTERVALS: "/igo/work/nabors/genomes/Drosophila_melanogaster/ENSEMBL/GTF/Drosophila_melanogaster.BDGP6.46.110.gtf.bed.rRNA.intervals",
+					GTF: "/igo/work/nabors/genomes/Drosophila_melanogaster/ENSEMBL/GTF/Drosophila_melanogaster.BDGP6.46.110.gtf",
 					GTAG: "dm6"
 				}
 		},