Merge pull request #5 from moka-guys/v1.2.0

changes for v1.2.0 (#5)

README.md

@@ -1,7 +1,7 @@
-# dnanexus_ED_readcount_analysis_v1.1.0
+# dnanexus_ED_readcount_analysis_v1.2.0
 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_v1.1.0 calculates readcounts for samples using panel of normals and intrabatch samples as reference.
+dnanexus_ED_readcount_analysis_v1.2.0 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.

dxapp.json

@@ -1,7 +1,10 @@
 {
-  "name": "ED_readcount_analysis_v1.1.0",
-  "title": "ED_readcount_analysis_v1.1.0",
-  "summary": "v1.1.0 - Step 1 of CNV calling using ExomeDepth",
+  "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",
+  "properties": {
+    "github release": "v1.2.0"
+  },
   "dxapi": "1.0.0",
   "inputSpec": [
     {
@@ -55,10 +58,16 @@
   ],
   "outputSpec": [
     {
-      "name": "exomedepth_output",
-      "label": "exomedepth output",
-      "help": "PDF output from ExomeDepth.",
-      "class": "array:file"
+      "name": "csv",
+      "label": "exomedepth CSV file",
+      "help": "CSV file containing CNVs",
+      "class": "file"
+    },
+    {
+      "name": "RData",
+      "label": "exomedepth RData file",
+      "help": "Readcount file",
+      "class": "file"
     }
   ],
   "runSpec": {
@@ -90,4 +99,4 @@
       }
     }
   }
-}
+}

src/code.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-# exomedepth_cnv_analysis_v1.1.0
+# exomedepth_cnv_analysis_v1.2.0
 
 # 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
@@ -10,10 +10,16 @@ set -e -x -o pipefail
 run=${project_name##*_}
 
 #read the DNA Nexus api key as a variable
-API_KEY=$(dx cat project-FQqXfYQ0Z0gqx7XG9Z2b4K43:mokaguys_nexus_auth_key)
+API_KEY_wquotes=$(echo $DX_SECURITY_CONTEXT |  jq '.auth_token')
+API_KEY=$(echo "$API_KEY_wquotes" | sed 's/"//g')
+echo "$API_KEY"
+
+output_RData_dir="/home/dnanexus/out/RData/exomedepth_output/${bedfile_prefix}"
+output_RData_file="${output_RData_dir}/${bedfile_prefix}_readCount.RData"
+output_CSV_dir="/home/dnanexus/out/csv/exomedepth_output/${bedfile_prefix}/"
 
 # make output dir and folder to hold downloaded files
-mkdir -p /home/dnanexus/out/exomedepth_output/exomedepth_output/$bedfile_prefix/ /home/dnanexus/to_test
+mkdir -p /home/dnanexus/to_test $output_CSV_dir $output_RData_dir
 
 mark-section "Downloading inputs"
 # download all inputs
@@ -39,7 +45,7 @@ echo "reference_genome="$reference_fasta
 echo "panel="$bamfile_pannumbers
 echo "bedfile_prefix="$bedfile_prefix
 echo "normals_RData="$normals_RData
-output_RData_file="/home/dnanexus/out/exomedepth_output/exomedepth_output/${bedfile_prefix}/${bedfile_prefix}_readCount.RData"
+
 
 mark-section "Download all relevant BAMs"
 # make and cd to test dir
@@ -73,10 +79,12 @@ cd /home/dnanexus
 
 mark-section "setting up Exomedepth docker image"
 # Location of the ExomeDepth docker file
-docker_file=project-ByfFPz00jy1fk6PjpZ95F27J:file-GYzKz400jy1yx101F34p8qj2
+docker_file_id=project-ByfFPz00jy1fk6PjpZ95F27J:file-GYzKz400jy1yx101F34p8qj2
 # download the docker file from 001_Tools...
-dx download $docker_file --auth "${API_KEY}"
-docker load -i '/home/dnanexus/seglh_exomedepth_87fa493.tgz'
+dx download $docker_file_id --auth "${API_KEY}"
+docker_file=$(dx describe ${docker_file_id} --name)
+DOCKERIMAGENAME=`tar xfO ${docker_file} manifest.json | sed -E 's/.*"RepoTags":\["?([^"]*)"?.*/\1/'`
+docker load < /home/dnanexus/"${docker_file}"
 #docker pull seglh/exomedepth:1111b6c
 mark-section "Calculate read depths using docker image"
 # docker run - mount the home directory as a share
@@ -90,7 +98,10 @@ mark-section "Calculate read depths using docker image"
 # The log (PanXXXXexomedepth_readCount.csv) written to same location as the $output_RData_file
 
 # Run ReadCount script in docker container
-docker run -v /home/dnanexus:/home/dnanexus seglh/exomedepth:87fa493 readCount.R $output_RData_file $reference_fasta $bedfile_path ${bam_list[@]} $normals_RData_path
+docker run -v /home/dnanexus:/home/dnanexus ${DOCKERIMAGENAME} readCount.R $output_RData_file $reference_fasta $bedfile_path ${bam_list[@]} $normals_RData_path
+
+# Move outputs into output folders to delocalise into dnanexus project
+mv $output_RData_dir/*.csv $output_CSV_dir
 
 # Upload results
-dx-upload-all-outputs
+dx-upload-all-outputs