update xml file

astrocyte_pkg.yml

@@ -76,29 +76,43 @@ workflow_modules:
 
 workflow_parameters:
 
+  - id: bams
+    type: files
+    required: true
+    description: |
+      Bam files of all samples
+
+  - id: peaks
+    type: files
+    required: true
+    description: |
+      Peak files of all samples. Bed format
+
   - id: design
     type: files
     required: true
     regex: ".*(csv)"
     description: |
-      A design file listing pairs of sample name and sample group.
+      A design file listing pairs of sample name and sample group. Must be in csv format
       Columns must include: SampleID,Tissue, Factor, Condition, Replicate, Peaks, bamReads, bamControl, ControlID, PeakCaller
 
-#  - id: genome
-#    type: select
-#    choices:
-#      - [ '/project/shared/bicf_workflow_ref/GRCh38', 'Human GRCh38']
-#      - [ '/project/shared/bicf_workflow_ref/GRCh37', 'Human GRCh37']
-#      - [ '/project/shared/bicf_workflow_ref/GRCm38', 'Mouse GRCh38']
-#    required: true
-#    description: |
-#      Reference genome for annotation
-
-#  - id: toppeak
-#    type: integer
-#    required: true
-#    description: |
-#      The number of top peaks to use for motif discovery.
+  - id: genome
+    type: select
+    choices:
+      - [ '/project/shared/bicf_workflow_ref/GRCh38', 'hg38']
+      - [ '/project/shared/bicf_workflow_ref/GRCh37', 'hg19']
+      - [ '/project/shared/bicf_workflow_ref/GRCm38', 'mm10']
+    required: true
+    description: |
+      Reference genome for annotation
+
+  - id: toppeak
+    type: integer
+    required: true
+    description: |
+      The number of top peaks to use for motif discovery.
+
+
 # -----------------------------------------------------------------------------
 # SHINY APP CONFIGURATION
 # -----------------------------------------------------------------------------