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| author | Justin Bedo <cu@cua0.org> | 2020-08-10 09:43:37 +1000 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2020-08-10 09:43:37 +1000 |
| commit | a3d00678c31829b96f503c701cdc3c47e6c2e23e (patch) | |
| tree | 44512e7ddf0fc946e885ef8c1bac36104f145edb /tools/hisat2-align.nix | |
| parent | bae57d22d7a626c12660f966eba0d2514d376860 (diff) | |
hisat2: add index prefix
Diffstat (limited to 'tools/hisat2-align.nix')
| -rw-r--r-- | tools/hisat2-align.nix | 2 |
1 files changed, 1 insertions, 1 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 \ |