From 3d3bc60a6b769b331c4623db6113b3b573c1b378 Mon Sep 17 00:00:00 2001
From: ameyner2 <alison.meynert@igmm.ed.ac.uk>
Date: Fri, 28 Aug 2020 17:04:51 +0100
Subject: [PATCH] Template for CRF NextSeq samples

---
 trio_whole_exome_bcbio_crf_template.yaml | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 trio_whole_exome_bcbio_crf_template.yaml

diff --git a/trio_whole_exome_bcbio_crf_template.yaml b/trio_whole_exome_bcbio_crf_template.yaml
new file mode 100644
index 0000000..0d87d96
--- /dev/null
+++ b/trio_whole_exome_bcbio_crf_template.yaml
@@ -0,0 +1,22 @@
+details:
+- algorithm:
+    platform: illumina
+    quality_format: standard
+    aligner: bwa
+    align_split_size: false
+    trim_reads: fastp
+    adapters: [nextera2, polyg]
+    mark_duplicates: true
+    realign: false
+    recalibrate: true
+    effects: vep
+    effects_transcripts: all
+    variantcaller: gatk-haplotype
+    indelcaller: false
+    remove_lcr: true
+    tools_on:
+    - vep_splicesite_annotations
+  analysis: variant2
+  genome_build: hg38
+upload:
+  dir: /scratch/u035/project/trio_whole_exome/analysis/output
-- 
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