From a259ff7f26458c0810741508df39a4b391ff18d4 Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Thu, 14 May 2020 16:47:08 -0400
Subject: Workflow fixes

---
 workflows/pangenome-generate/pangenome-generate.cwl | 7 ++++---
 workflows/tools                                     | 2 +-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/workflows/pangenome-generate/pangenome-generate.cwl b/workflows/pangenome-generate/pangenome-generate.cwl
index 1d49904..ad8b27f 100644
--- a/workflows/pangenome-generate/pangenome-generate.cwl
+++ b/workflows/pangenome-generate/pangenome-generate.cwl
@@ -57,8 +57,9 @@ steps:
     in:
       target: dedup/reads_dedup
       query: dedup/reads_dedup
-      outputCIGAR:
-        default: true
+      outputCIGAR: {default: true}
+      preset: {default: asm20}
+      miniWinSize: {default: 1}
     out: [alignments]
     run: ../tools/minimap2/minimap2_paf.cwl
   induceGraph:
@@ -106,7 +107,7 @@ steps:
     out: [ bins, pangenome_sequence ]
   index_paths:
     label: Create path index
-    run : ../tools/odgi/odgi_pathindex.cwl
+    run: ../tools/odgi/odgi_pathindex.cwl
     in:
       sparse_graph_index: buildGraph/odgiGraph
     out: [ indexed_paths ]
diff --git a/workflows/tools b/workflows/tools
index 659e174..1ecbfef 160000
--- a/workflows/tools
+++ b/workflows/tools
@@ -1 +1 @@
-Subproject commit 659e174d0d42ed6b9afd79d9e6f68e225c526d1e
+Subproject commit 1ecbfefa2c064c9b99765a4fb0f84f84e28d35c9
-- 
cgit v1.2.3