From 352c7afc0d512834f2249dad5f68b295834d5c3f Mon Sep 17 00:00:00 2001
From: Nareh Sahakian <sahakian@broadinstitute.org>
Date: Mon, 13 May 2024 21:09:48 -0400
Subject: [PATCH] add pipline_inputs subdir to location of index files again

---
 pipelines/skylab/snm3C/snm3C.wdl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pipelines/skylab/snm3C/snm3C.wdl b/pipelines/skylab/snm3C/snm3C.wdl
index ebebc74a6f..1f40a2d392 100644
--- a/pipelines/skylab/snm3C/snm3C.wdl
+++ b/pipelines/skylab/snm3C/snm3C.wdl
@@ -412,9 +412,9 @@ task Hisat_paired_end {
           start=$(date +%s)
           echo "Run hisat"
           if [ ~{cromwell_root_dir} = "gcp" ]; then
-            hisat_index_file_dir="~{cromwell_root_dir}/pipeline_inputs/$genome_fa_basename"
+            hisat_index_file_dir="~{cromwell_root_dir}/$genome_fa_basename"
           else
-            hisat_index_file_dir="$WORKING_DIR/$genome_fa_basename"
+            hisat_index_file_dir="$WORKING_DIR/pipeline_inputs/$genome_fa_basename"
           fi
           echo "hisat_index_file_dir: $hisat_index_file_dir"