Merge pull request #7 from moka-guys/v1.3.0

V1.3.0 (#7)

README.md

@@ -1,14 +1,14 @@
-# dnanexus_ED_readcount_analysis_v1.2.0
+# dnanexus_ED_readcount_analysis_v1.3.0
 Exome depth is run in two stages. Firstly, read counts are calculated, before CNVs are called using the read counts. Read counts are calculated over the entire genome whereas the CNV calling can be performed using a subpanel.
 
-dnanexus_ED_readcount_analysis_v1.2.0 calculates readcounts for samples using panel of normals and intrabatch samples as reference.
+dnanexus_ED_readcount_analysis_v1.3.0 calculates readcounts for samples using panel of normals and intrabatch samples as reference.
 
 # What does the app do?
 This app runs the read count calculation stage.
 
 Using the provided DNANexus project and the list of Pan numbers the app downloads BAMs and BAI.
 
-A Docker image containing Exome depth is downloaded from 001 - The Exomedepth image taken from https://github.com/moka-guys/seglh-cnv/releases/tag/v2.0.0
+A Docker image containing Exome depth is downloaded from 001 - The Exomedepth image taken from https://github.com/moka-guys/seglh-cnv/releases/tag/v2.1.0
 
 The `readCount.R` script is then called, producing a readcount file (`PanXXXXexomedepth_readCount.RData`) which can be used as an input for the ED_cnv_calling app https://github.com/moka-guys/dnanexus_ED_cnv_calling
 

dxapp.json

@@ -1,9 +1,9 @@
 {
-  "name": "ED_readcount_analysis_v1.2.0",
-  "title": "ED_readcount_analysis_v1.2.0",
-  "summary": "v1.2.0 - Step 1 of CNV calling using ExomeDepth",
+  "name": "ED_readcount_analysis_v1.3.0",
+  "title": "ED_readcount_analysis_v1.3.0",
+  "summary": "v1.3.0 - Step 1 of CNV calling using ExomeDepth",
   "properties": {
-    "github release": "v1.2.0"
+    "github release": "v1.3.0"
   },
   "dxapi": "1.0.0",
   "inputSpec": [

src/code.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-# exomedepth_cnv_analysis_v1.2.0
+# exomedepth_cnv_analysis_v1.3.0
 
 # The following line causes bash to exit at any point if there is any error
 # and to output each line as it is executed -- useful for debugging
@@ -79,7 +79,7 @@ cd /home/dnanexus
 
 mark-section "setting up Exomedepth docker image"
 # Location of the ExomeDepth docker file
-docker_file_id=project-ByfFPz00jy1fk6PjpZ95F27J:file-GYzKz400jy1yx101F34p8qj2
+docker_file_id=project-ByfFPz00jy1fk6PjpZ95F27J:file-Gbjy9yj0JQXkKB8bfFz856V6
 # download the docker file from 001_Tools...
 dx download $docker_file_id --auth "${API_KEY}"
 docker_file=$(dx describe ${docker_file_id} --name)