0.1.2 proper zipping

manifest.json

@@ -2,7 +2,7 @@
 	"name": "hasl-decode",
 	"label": "HASL Decoder: Hadamard-encoded ASL (HASL) processing pipeline",
 	"description": "Hadamard-encoded multi-delay ASL data(HASL) processing pipeline for measuring cerebrovascular reactivity. Decodes the Hadamard matrix into three post-labelling delays and calculates cerebral blood flow, arterial transit time and transit time-corrected cerebral blood flow.",
-	"version": "0.1.1_0.1.1",
+	"version": "0.1.1_0.1.2",
 	"inputs": {
 		"asl": {
 			"base": "file",
@@ -24,7 +24,6 @@
 			"type": "boolean"
 		},
 		"stimulus_start": {
-			"default": 31,
 			"description": "Timepoint when CO2 stimulus starts. (hyperC02 must be set to true for this to apply.)",
 			"optional": true,
 			"type": "integer"
@@ -45,7 +44,7 @@
 	"custom": {
 		"gear-builder": {
 			"category": "analysis",
-			"image": "willtack/hasl:0.1.1"
+			"image": "willtack/hasl:0.1.2"
 		},
 		"flywheel": {
 			"suite": "BrainScienceCenter"

run

@@ -78,7 +78,7 @@ else
   cd $OUTPUT_DIR
   mkdir results
   cp * results/
-  zip results.zip results
+  zip -r results.zip results
   rm -rf results
   rm -rf MPRAGE ASL M0 # remove the intermediate directories. just keep the derived maps
   echo -e "$CONTAINER  Wrote: `ls`"