From 10c7966ed33e1b2c76cd6a8518f8ad4922d12c46 Mon Sep 17 00:00:00 2001
From: natashapinto <natasha.b.pinto@gmail.com>
Date: Mon, 2 Oct 2023 15:28:57 +0100
Subject: [PATCH] changes for v1.2.0

---
 README.md   |  4 ++--
 dxapp.json  | 25 +++++++++++++++++--------
 src/code.sh | 29 ++++++++++++++++++++---------
 3 files changed, 39 insertions(+), 19 deletions(-)

diff --git a/README.md b/README.md
index a7522ac..c9c8faa 100644
--- a/README.md
+++ b/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.
diff --git a/dxapp.json b/dxapp.json
index df418d5..ed769bb 100644
--- a/dxapp.json
+++ b/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 @@
       }
     }
   }
-}
+}
\ No newline at end of file
diff --git a/src/code.sh b/src/code.sh
index 1da6a8e..9ebceb7 100644
--- a/src/code.sh
+++ b/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
\ No newline at end of file