set up v86

conchoecia · May 27, 2020 · ed5b543 · ed5b543
1 parent c218b6c
commit ed5b543
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Showing 3 changed files with 13,560 additions and 5 deletions.
diff --git a/annotation/Snakefile b/annotation/Snakefile
@@ -42,7 +42,7 @@ with gzip.open(REF, "rt") as f:
 #!!!!
 #!!!!!
 #Prefix must not have underscores or periods
-PREFIX   = "Hcv1av85" #< DO NOT. PUT an UNDERSCORE or a PERIOD in this PREFIX!
+PREFIX   = "Hcv1av86" #< DO NOT. PUT an UNDERSCORE or a PERIOD in this PREFIX!
 # ^ PREFIX MUST NOT HAVE UNDERSCORES OR PERIODS. ^
 #!!!!!
 #!!!!
@@ -51,11 +51,11 @@ PREFIX   = "Hcv1av85" #< DO NOT. PUT an UNDERSCORE or a PERIOD in this PREFIX!
 #!
 CSV      = "raw_files/Hcal_annotation_v85.csv"
 GAN      = "Hcv1"
-AV       = "v85" #the assembly version
+AV       = "v86" #the assembly version
 FLNC     = "raw_files/GLO64_flnc.fastq.gz"
 PILONJAR = "raw_files/pilon-1.22.jar"
-RNAF     = "raw_files/Hc1_lib17_run1_ILL_RNAseq_R1.fastq.gz"
-RNAR     = "raw_files/Hc1_lib17_run1_ILL_RNAseq_R2.fastq.gz"
+RNAF     = "/bigdata/raw/rna_reads/Project_STDS_L7_H1546P_Schultz/DS242_S98_L007_R1_001.fastq.gz"
+RNAR     = "/bigdata/raw/rna_reads/Project_STDS_L7_H1546P_Schultz/DS242_S98_L007_R2_001.fastq.gz"
 # VCF file for the whole genome
 gVCFs     = expand("../phasing/final_output/phased_by_chromosome/largest_blocks.hap.phased.{chrs}.vcf.gz", chrs = chroms)
 

diff --git a/annotation/make_release.sh b/annotation/make_release.sh
@@ -1,5 +1,5 @@
 #!/bin/bash
-RELEASE=Hcv1av85
+RELEASE=Hcv1av86
 mkdir ${RELEASE}_release
 find ./final_output/ -type f -name "*" -exec cp {} ${RELEASE}_release \;
 rm ${RELEASE}_release/*vcf*