From a3d00678c31829b96f503c701cdc3c47e6c2e23e Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Mon, 10 Aug 2020 09:43:37 +1000
Subject: hisat2: add index prefix

---
 tools/hisat2-align.nix | 2 +-
 tools/hisat2-index.nix | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

(limited to 'tools')

diff --git a/tools/hisat2-align.nix b/tools/hisat2-align.nix
index 277b499..dfd9601 100644
--- a/tools/hisat2-align.nix
+++ b/tools/hisat2-align.nix
@@ -27,7 +27,7 @@ in stage {
     if [[ $cores -lt 1 ]] ; then
       cores=1
     fi
-    hisat2 ${optionalString (flags != null) flags} -p $cores -x ${hisat2.index indexAttrs ref}/ \
+    hisat2 ${optionalString (flags != null) flags} -p $cores -x ${hisat2.index indexAttrs ref}/index \
       ${if input2 != null then "-1 ${fq input1} -2 ${fq input2}" else "-U ${fq input1}"} \
       ${optionalString bamOutput "| samtools view -b"} \
       | samtools sort -n \
diff --git a/tools/hisat2-index.nix b/tools/hisat2-index.nix
index 82935eb..ffdb4ed 100644
--- a/tools/hisat2-index.nix
+++ b/tools/hisat2-index.nix
@@ -21,7 +21,7 @@ stage {
     mkdir $out
     hisat2-build -p $NIX_BUILD_CORES ${optionalString (flags != null) flags} \
       ${optionalString (gtf != null) "--ss ${hisat2.extractSpliceSites extractSpliceSitesAttrs gtf} --exon ${hisat2.extractExons extractExonsAttrs gtf}"} \
-      ref.fa $out/
+      ref.fa $out/index
   '';
   passthru.multicore = true;
 }
-- 
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