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authorJustin Bedo <cu@cua0.org>2020-08-10 09:43:37 +1000
committerJustin Bedo <cu@cua0.org>2020-08-10 09:43:37 +1000
commita3d00678c31829b96f503c701cdc3c47e6c2e23e (patch)
tree44512e7ddf0fc946e885ef8c1bac36104f145edb
parentbae57d22d7a626c12660f966eba0d2514d376860 (diff)
hisat2: add index prefix
-rw-r--r--tools/hisat2-align.nix2
-rw-r--r--tools/hisat2-index.nix2
2 files changed, 2 insertions, 2 deletions
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;
}