From 9c0315addb194e2360c6fe76d53a9947d3866fab Mon Sep 17 00:00:00 2001
From: Olga Botvinnik <olga.botvinnik@gmail.com>
Date: Fri, 31 May 2019 13:17:48 -0700
Subject: [PATCH] Use flat nongzipped files

---
 conf/czbiohub.config | 52 ++++++++++++++++++++++----------------------
 1 file changed, 26 insertions(+), 26 deletions(-)

diff --git a/conf/czbiohub.config b/conf/czbiohub.config
index 1c788b9..d51c6f2 100644
--- a/conf/czbiohub.config
+++ b/conf/czbiohub.config
@@ -47,59 +47,59 @@ params {
   // GENCODE GTF and fasta files
   genomes {
     'GRCh38' {
-      fasta   = "${params.gencode_base}/human/v29/GRCh38.p12.genome.fa.gz"
-      gtf     = "${params.gencode_base}/human/v29/gencode.vM19.annotation.gtf.gz"
+      fasta   = "${params.gencode_base}/human/v29/GRCh38.p12.genome.fa"
+      gtf     = "${params.gencode_base}/human/v29/gencode.vM19.annotation.gtf"
     }
     'GRCm38' {
-      fasta   = "${params.gencode_base}/mouse/vM19/GRCm38.p6.genome.fa.gz"
-      gtf     = "${params.gencode_base}/mouse/vM19/gencode.vM19.annotation.gtf.gz"
+      fasta   = "${params.gencode_base}/mouse/vM19/GRCm38.p6.genome.fa"
+      gtf     = "${params.gencode_base}/mouse/vM19/gencode.vM19.annotation.gtf"
     }
   }
 
   transgenes {
     'ChR2' {
-      fasta   = "${params.transgenes_base}/ChR2/ChR2.fa.gz"
-      gtf     = "${params.transgenes_base}/ChR2/ChR2.gtf.gz"
+      fasta   = "${params.transgenes_base}/ChR2/ChR2.fa"
+      gtf     = "${params.transgenes_base}/ChR2/ChR2.gtf"
     }
     'Cre' {
-      fasta   = "${params.transgenes_base}/Cre/Cre.fa.gz"
-      gtf     = "${params.transgenes_base}/Cre/Cre.gtf.gz"
+      fasta   = "${params.transgenes_base}/Cre/Cre.fa"
+      gtf     = "${params.transgenes_base}/Cre/Cre.gtf"
     }
     'ERCC' {
-      fasta   = "${params.transgenes_base}/ERCC92/ERCC92.fa.gz"
-      gtf     = "${params.transgenes_base}/ERCC92/ERCC92.gtf.gz"
+      fasta   = "${params.transgenes_base}/ERCC92/ERCC92.fa"
+      gtf     = "${params.transgenes_base}/ERCC92/ERCC92.gtf"
     }
     'GCaMP6m' {
-      fasta   = "${params.transgenes_base}/GCaMP6m/GCaMP6m.fa.gz"
-      gtf     = "${params.transgenes_base}/GCaMP6m/GCaMP6m.gtf.gz"
+      fasta   = "${params.transgenes_base}/GCaMP6m/GCaMP6m.fa"
+      gtf     = "${params.transgenes_base}/GCaMP6m/GCaMP6m.gtf"
     }
     'GFP' {
-      fasta   = "${params.transgenes_base}/Gfp/Gfp.fa.gz"
-      gtf     = "${params.transgenes_base}/Gfp/Gfp.gtf.gz"
+      fasta   = "${params.transgenes_base}/Gfp/Gfp.fa"
+      gtf     = "${params.transgenes_base}/Gfp/Gfp.gtf"
     }
     'NpHR' {
-      fasta   = "${params.transgenes_base}/NpHR/NpHR.fa.gz"
-      gtf     = "${params.transgenes_base}/NpHR/NpHR.gtf.gz"
+      fasta   = "${params.transgenes_base}/NpHR/NpHR.fa"
+      gtf     = "${params.transgenes_base}/NpHR/NpHR.gtf"
     }
     'RCaMP' {
-      fasta   = "${params.transgenes_base}/RCaMP/RCaMP.fa.gz"
-      gtf     = "${params.transgenes_base}/RCaMP/RCaMP.gtf.gz"
+      fasta   = "${params.transgenes_base}/RCaMP/RCaMP.fa"
+      gtf     = "${params.transgenes_base}/RCaMP/RCaMP.gtf"
     }
     'RGECO' {
-      fasta   = "${params.transgenes_base}/RGECO/RGECO.fa.gz"
-      gtf     = "${params.transgenes_base}/RGECO/RGECO.gtf.gz"
+      fasta   = "${params.transgenes_base}/RGECO/RGECO.fa"
+      gtf     = "${params.transgenes_base}/RGECO/RGECO.gtf"
     }
     'Tdtom' {
-      fasta   = "${params.transgenes_base}/Tdtom/Tdtom.fa.gz"
-      gtf     = "${params.transgenes_base}/Tdtom/Tdtom.gtf.gz"
+      fasta   = "${params.transgenes_base}/Tdtom/Tdtom.fa"
+      gtf     = "${params.transgenes_base}/Tdtom/Tdtom.gtf"
     }
     'Car-T' {
-      fasta   = "${params.transgenes_base}/car-t/car-t.fa.gz"
-      gtf     = "${params.transgenes_base}/car-t/car-t.gtf.gz"
+      fasta   = "${params.transgenes_base}/car-t/car-t.fa"
+      gtf     = "${params.transgenes_base}/car-t/car-t.gtf"
     }
     'zsGreen' {
-      fasta   = "${params.transgenes_base}/zsGreen/zsGreen.fa.gz"
-      gtf     = "${params.transgenes_base}/zsGreen/zsGreen.gtf.gz"
+      fasta   = "${params.transgenes_base}/zsGreen/zsGreen.fa"
+      gtf     = "${params.transgenes_base}/zsGreen/zsGreen.gtf"
     }
   }
 }