From c7817240ebe84087daeb07f33c4d1671a9cb8cfb Mon Sep 17 00:00:00 2001 From: darrelln32 Date: Sun, 21 Apr 2024 11:06:12 -0400 Subject: [PATCH] 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 --- scripts/LaunchMetrics.py | 2 +- scripts/run_param_config.py | 14 +++++++------- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/scripts/LaunchMetrics.py b/scripts/LaunchMetrics.py index 7789d20..014919a 100644 --- 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 index ef2e78a..a8f4654 100644 --- 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" } },