From 7aed228a809f23fe56bad83f5b5ac6571a6a6188 Mon Sep 17 00:00:00 2001
From: ameyner2 <alison.meynert@igmm.ed.ac.uk>
Date: Wed, 9 Sep 2020 10:36:32 +0100
Subject: [PATCH] Added CRF configuration file

---
 trio_whole_exome_crf_config.sh | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 trio_whole_exome_crf_config.sh

diff --git a/trio_whole_exome_crf_config.sh b/trio_whole_exome_crf_config.sh
new file mode 100644
index 0000000..ce14950
--- /dev/null
+++ b/trio_whole_exome_crf_config.sh
@@ -0,0 +1,21 @@
+#!/usr/bin/bash
+#
+# Basic configuration options for trio WES pipeline
+#
+
+SCRIPTS=/home/u035/project/scripts
+BCBIO_TEMPLATE=$SCRIPTS/trio_whole_exome_bcbio_crf_template.yaml
+TARGET=/home/u035/project/resources/Twist_Exome_RefSeq_targets_hg38.plus15bp.bed
+DOWNLOAD_DIR=/scratch/u035/project/trio_whole_exome/data
+REFERENCE_GENOME=/home/u035/project/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa
+
+BASE=/scratch/u035/project/trio_whole_exome/analysis
+PARAMS_DIR=$BASE/params
+READS_DIR=$BASE/reads
+CONFIG_DIR=$BASE/config
+WORK_DIR=$BASE/work
+OUTPUT_DIR=$BASE/output
+
+ARCHIVE_DIR=/archive/u035/trio_whole_exome
+
+export PATH=/home/u035/project/software/bcbio/tools/bin:$PATH
-- 
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