From a25480f03c3a92b58a5e94f35ced06d6664c6eb0 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Mon, 26 Mar 2018 09:24:24 -0500
Subject: [PATCH] add support mouse

---
 workflow/main.nf         | 4 ++--
 workflow/process_scripts | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/workflow/main.nf b/workflow/main.nf
index dee4492..39b0c00 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -64,7 +64,7 @@ else {
 spltnames
  .splitCsv()
  .filter { fileMap.get(it[1]) != null }
- .map { it -> tuple(it[0], fileMap.get(it[1]),fileMap.get(it[1])) }
+ .map { it -> tuple(it[0], fileMap.get(it[1]),'') }
  .set { read }
 }
 if( ! read ) { error "Didn't match any input files with entries in the design file" }
@@ -232,7 +232,7 @@ process gatkbam {
   output:
   set file("${pair_id}.final.bam"),file("${pair_id}.final.bai") into gatkbam
   when:
-  params.align == 'hisat'
+  params.align == 'hisat' && $index_path == '/project/shared/bicf_workflow_ref/GRCh38/'
   script:
   """
   bash $baseDir/process_scripts/variants/gatkrunner.sh -a gatkbam_rna -b $rbam -r ${index_path}/hisat_index -p $pair_id
diff --git a/workflow/process_scripts b/workflow/process_scripts
index b6d2f68..012a37c 160000
--- a/workflow/process_scripts
+++ b/workflow/process_scripts
@@ -1 +1 @@
-Subproject commit b6d2f6898ecc1890b4df305e9505bdaa5eace4a6
+Subproject commit 012a37c5f66ad4c20312642904416c4c493fa75e
-- 
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