add parameter

README.md

@@ -43,8 +43,32 @@ choppy install YaqingLiu/CNVkit
           "oss://choppy-cromwell-result/...bai",
           "oss://choppy-cromwell-result/...bai"
     ],
-	"sample_id": "..."
+	"sample_id": "...",
+    "method": "...",
+    "reference": "..." # this parameter is optional
 }
 ```
+***Note***
+```shell
+-m {hybrid,amplicon,wgs}, --seq-method {hybrid,amplicon,wgs}, --method {hybrid,amplicon,wgs}
+        Sequencing assay type: hybridization capture
+        ('hybrid'), targeted amplicon sequencing
+        ('amplicon'), or whole genome sequencing ('wgs').
+        Determines whether and how to use antitarget bins.
+
+To reuse an existing reference or create a new :
+-r REFERENCE, --reference REFERENCE
+        Copy number reference file (.cnn).
+--output-reference FILENAME
+        Output filename/path for the new reference file
+        being created. (If given, ignores the 
+        -o/--output-dir option and will write the file to
+        the given path. Otherwise, "reference.cnn" will
+        be created in the current directory or specified
+        output directory.)
+```
 ## Output
-A segment file and some intermediate *.cnn/cns will be generated, and the segment file can be imported into IGV.
+1. *.cnn/cns of each sample.
+2. A whole-genome copy ratio profile as a PDF scatter plot.
+3. An ideogram of copy ratios on chromosomes as a PDF.
+4. A segment file which can be imported into IGV.

inputs

@@ -7,6 +7,8 @@
   "{{ project_name }}.fasta": "{{ fasta }}",
   "{{ project_name }}.faidx": "{{ faidx }}",
   "{{ project_name }}.ref_flat": "{{ ref_flat }}",
+  "{{ project_name }}.method": "{{ method }}",
+  "{{ project_name }}.reference": "{{ reference }}",
   "{{ project_name }}.docker": "{{ docker }}",
   "{{ project_name }}.bed": "{{ bed }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",

tasks/batch.wdl

@@ -9,6 +9,8 @@ task batch {
     File fasta
     File ref_flat
     File access_bed
+    File? reference
+    String method
     String docker
     String cluster_config
     String disk_size
@@ -27,8 +29,10 @@ task batch {
         cnvkit.py batch ${sep=' ' tumor_bam} --normal ${sep=' ' normal_bam} \
         --targets ${bed} --annotate ${ref_flat} \
         --fasta hg38.fa --access ${access_bed} \
-        --output-reference ${sample_id}.reference.cnn --output-dir /cromwell_root/tmp/cnvkit/results/ \
-        --diagram --scatter
+        --method ${method} \
+        --reference ${reference} --output-reference ~/${sample_id}.reference.cnn \
+        --output-dir ./results/ \
+        --drop-low-coverage --diagram --scatter
     >>>
 
     runtime { 

workflow.wdl

@@ -12,6 +12,8 @@ workflow {{ project_name }} {
 	File faidx
 	File fasta
     File ref_flat
+    File? reference
+    String method
     String docker
     String cluster_config
     String disk_size
@@ -31,6 +33,8 @@ workflow {{ project_name }} {
         fasta = fasta,
         faidx = faidx,
         ref_flat = ref_flat,
+        method = method,
+        reference = reference,
         tumor_bam = tumor_bam,
         tumor_bai = tumor_bai,
         normal_bam = normal_bam,