Change outut structure

README.md

@@ -65,6 +65,6 @@ The samplesheet specified in the `input` parameter should be a CSV file with the
 - `convert`: [boolean] Should the image be converted to a OME-TIFF
 - `he`: [boolean] Is the image a H&E image
 - `minerva`: [boolean] Should a Minerva story be generated
-- `miniatuee`: [boolean] Should a Miniature thumbnail be generated
+- `miniature`: [boolean] Should a Miniature thumbnail be generated
 - `id`: *optional* [string] A custom identifier to replace image simpleName in output directory structure 
 

data/test_samplesheet.csv

@@ -1,3 +1,3 @@
 image,convert,he,minerva,miniature,id
-datas/exemplar-001_small.tif,true,false,true,true,cycif
+data/exemplar-001_small.tif,true,false,true,true,cycif
 data/CMU-1-Small-Region.svs,true,true,true,true,h_and_e

modules/autominerva_story.nf

@@ -5,9 +5,9 @@ process autominerva_story {
       tuple val(meta), file(image) 
   output:
       tuple val(meta), file(image), file('story.json')
-  publishDir "$params.outdir/$workflow.runName",
+  publishDir "$params.outdir",
       pattern: 'story.json',
-      saveAs: {filename -> "${meta.id}/$workflow.runName/story.json"}
+      saveAs: {filename -> "${meta.id}/story.json"}
   stub: 
   """
   touch story.json

modules/make_miniature.nf

@@ -5,8 +5,8 @@ process make_miniature {
       tuple val(meta), file(image) 
   output:
       tuple val(meta), file('miniature.jpg')
-  publishDir "$params.outdir/$workflow.runName",
-    saveAs: {filename -> "${meta.id}/$workflow.runName/thumbnail.jpg"}
+  publishDir "$params.outdir",
+    saveAs: {filename -> "${meta.id}/thumbnail.jpg"}
   stub:
   """
   mkdir data

modules/render_pyramid.nf

@@ -5,8 +5,8 @@ process render_pyramid {
       tuple val(meta), file(image), file (story)
   output:
       tuple val(meta), path('minerva')
-  publishDir "$params.outdir/$workflow.runName",
-    saveAs: {filename -> "${meta.id}/$workflow.runName/minerva"}
+  publishDir "$params.outdir",
+    saveAs: {filename -> "${meta.id}/minerva"}
   stub:
   """
   mkdir minerva