Minor updates to workflow Mark I (#312)

This update fixes a small bug and updates a default value in workflow Mark I.
kevlar-dev · Dec 12, 2018 · 686e154 · 686e154
1 parent 76a82fc
commit 686e154
Show file tree

Hide file tree

Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/kevlar/workflows/mark-I/Snakefile b/kevlar/workflows/mark-I/Snakefile
@@ -301,7 +301,7 @@ rule localize:
         'Logs/localize.log'
     threads: 1
     message: 'Compute reference target sequences for each partition.'
-    shell: 'kevlar --tee --logfile {output[1]} localize --delta {config[localize][delta]} --seed-size {config[localize][seedsize]} --include {config[localize][seqpattern]} --out {output[0]} {input[0]} {input[1]}'
+    shell: 'kevlar --tee --logfile {output[1]} localize --delta {config[localize][delta]} --seed-size {config[localize][seedsize]} --include \'{config[localize][seqpattern]}\' --out {output[0]} {input[0]} {input[1]}'
 
 
 rule call:

diff --git a/kevlar/workflows/mark-I/config.json b/kevlar/workflows/mark-I/config.json
@@ -53,6 +53,7 @@
     "localize": {
         "seedsize": 51,
         "delta": 50,
-        "seqpattern": "."
+        "seqpattern": ".",
+        "maxdiff": 10000
     }
 }