Merge pull request #2 from moka-guys/v1.1.0

dual reporting changes (#2)

README.md

@@ -1,4 +1,4 @@
-# dnanexus_ED_cnv_analysis_v1.0.0
+# dnanexus_ED_cnv_analysis_v1.1.0
 Performs CNV calling using ExomeDepth.
 
 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.
@@ -8,8 +8,7 @@ This app runs the CNV calling stage.
 
 # How the app works?
 
-A Docker image containing Exome depth is downloaded from 001 - In this release [#1220d31](https://github.com/moka-guys/seglh-cnv/tree/1220d31e2eed1d4488eb461e70615a0fad8b5eb1) is used.
-
+A Docker image containing Exome depth is downloaded from 001 - The image is taken from https://github.com/moka-guys/seglh-cnv/releases/tag/v2.0.0
 The app takes in a readcount file generated by https://github.com/moka-guys/dnanexus\_ED\_readcount_analysis, the docker image will pick the most appropriate reference samples and run exomedepth for a given sample. 
 
 
@@ -18,9 +17,9 @@ For further details on the usage of the docker image please refer to https://git
 # Input
 - DNAnexus project name where the BAM and the indexes are stored (BAMs/BAIs MUST be present in the /output folder)
 - Readcount file generated using https://github.com/moka-guys/dnanexus\_ED\_readcount_analysis
-- QC file containing QC parameters (Optional) - generated using https://github.com/moka-guys/dnanexus\_ED\_readcount_analysis
 - List of comma seperated pan numbers (Pan4127,Pan4129,Pan4130,Pan4049)
 - Test specific BED file
+Note: Transitional probability is set to 0.01, the default value is 0.001 (too many false positives during testing).
 See CLI command below for an example of inputs.
 
 # Output
@@ -35,13 +34,12 @@ See CLI command below for an example of inputs.
 The app can be run from the dx CLI.  The example below shows the code used to run test samples through this app:
 
 ```bash
-dx run project-G0pKxX80pgqFk9Vy8p6vQbKv:applet-G7B5Zxj0pgq9Q8JfP0jpY3y4 -iproject_name=003_220103_exomeDepth_calling_test -ireadcount_file=project-G6jb1k807Xjj1J984K6kfP13:file-G6kg5q80gvvz37qZ4ZPbvZ8Q -ibamfile_pannumbers=Pan4127,Pan4129,Pan4130,Pan4049 -isubpanel_bed=project-ByfFPz00jy1fk6PjpZ95F27J:file-G6kZpqQ0jy1q1Zk94G3qbVyV -iQC_file=project-G6jb1k807Xjj1J984K6kfP13:file-G66X1Z80p6PG52GFK4zfpY7y
-
+dx run project-G0pKxX80pgqFk9Vy8p6vQbKv:applet-G7B5Zxj0pgq9Q8JfP0jpY3y4 -iproject_name=003_220103_exomeDepth_calling_test -ireadcount_file=project-G6jb1k807Xjj1J984K6kfP13:file-G6kg5q80gvvz37qZ4ZPbvZ8Q -ibamfile_pannumbers=Pan4127,Pan4129,Pan4130,Pan4049 -isubpanel_bed=project-ByfFPz00jy1fk6PjpZ95F27J:file-G6kZpqQ0jy1q1Zk94G3qbVyV 
 ```
 # Debugging
 
 For debugging issues with the `docker` image it can be helpful to `ssh` into a 'held for debugging' job in DNA nexus and run the `docker` image in interactive mode:
 
 ```bash
-docker run -v /home/dnanexus:/home/dnanexus/ --rm -it --entrypoint /bin/bash seglh/exomedepth:1220d31
+docker run -v /home/dnanexus:/home/dnanexus/ --rm -it --entrypoint /bin/bash seglh/exomedepth:87fa493
 ```

dxapp.json

@@ -1,7 +1,7 @@
 {
-  "name": "ED_cnv_calling_v1.0.0",
-  "title": "ED_cnv_calling_v1.0.0",
-  "summary": "v1.0.0 - Performs CNV calling using ExomeDepth",
+  "name": "ED_cnv_calling_v1.1.0",
+  "title": "ED_cnv_calling_v1.1.0",
+  "summary": "v1.1.0 - Performs CNV calling using ExomeDepth",
   "dxapi": "1.0.0",
   "inputSpec": [
     {
@@ -18,14 +18,6 @@
       "patterns": ["*.RData"],
       "optional": false
     },
-    {
-      "name": "QC_file",
-      "label": "QC_file",
-      "help": "QC metrics specific for each panel",
-      "class": "file",
-      "patterns": ["*.RData"],
-      "optional": true
-    },
     {
       "name": "bamfile_pannumbers",
       "label": "bamfile_pannumbers",
@@ -45,7 +37,7 @@
     {
       "name": "exomedepth_output",
       "label": "exomedepth output",
-      "help": "PDF output from ExomeDepth.",
+      "help": "outputs from ExomeDepth.",
       "class": "array:file"
     }
   ],

src/code.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-# exomedepth_cnv_analysis_v1.0.0
+# exomedepth_cnv_analysis_v1.1.0
 
 # 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
@@ -16,7 +16,7 @@ readcount_file_name=$(dx describe --name "$readcount_file")
 subpanel_bed_prefix=$(echo "$subpanel_bed_name" | sed -r  's/^[^0-9]*(Pan[0-9]+).*/\1/')
 
 # Location of the ExomeDepth docker file
-docker_file=project-ByfFPz00jy1fk6PjpZ95F27J:file-G6kfZYQ0jy1vZ0BF33KZpQjJ
+docker_file=project-ByfFPz00jy1fk6PjpZ95F27J:file-GYzKz400jy1yx101F34p8qj2
 
 #read the DNA Nexus api key as a variable
 API_KEY=$(dx cat project-FQqXfYQ0Z0gqx7XG9Z2b4K43:mokaguys_nexus_auth_key)
@@ -81,7 +81,7 @@ cd ..
 mark-section "setting up Exomedepth docker image"
 # download the docker file from 001_Tools...
 dx download $docker_file --auth "${API_KEY}"
-docker load -i '/home/dnanexus/seglh_exomedepth_1220d31.tgz'
+docker load -i '/home/dnanexus/seglh_exomedepth_87fa493.tgz'
 
 mark-section "Run CNV analysis using docker image"
 
@@ -95,26 +95,33 @@ do
 samplename=$(basename "$bam" _R1_001.bam) 
 echo "samplename:" "$samplename"
 echo "bam:" "$bam"
-echo "subpanel:" "$subpanel_bed_name" 
-
-# Handle optional argument relating to QC file
-if [ -z "$QC_file" ]; then
-	echo "Optional QC file not provided by user"
-	bam_and_QC_command="$bam":"$samplename"
-	else
-	QC_file_path="/home/dnanexus/in/QC_file/*.RData"
-	bam_and_QC_command="$bam:$samplename $QC_file_path"
+echo "subpanel:" "$subpanel_bed_name"
+echo "trans_prob:" "$trans_prob"
+
+# Check which QC file to you
+#Extract panel type from samplename
+#split samplename on '_'
+panelname="$(echo $samplename | cut -d'_' -f6)"
+echo $panelname
+if [[ "$panelname" == *VCP1* ]]; then 
+	QC_file="vcp1_qc.RData";
+elif [[ "$panelname" == *VCP2* ]]; then
+	QC_file="vcp2_qc.RData";
+elif [[ "$panelname" == *VCP3* ]]; then
+	QC_file="vcp3_qc.RData";
 fi
 
+#test
+echo "RDATA = " "$readcount_file_name"
 #for each bam run exomedepth - the string in the format v1.0.0 will be concatenated to the ouput as the app version
 docker run -v /home/dnanexus:/home/dnanexus/ \
-	--rm  seglh/exomedepth:1220d31 \
+	--rm  seglh/exomedepth:87fa493 \
 	exomeDepth.R \
-	'v1.0.0' \
+	'v1.1.0' \
 	/home/dnanexus/out/exomedepth_output/exomedepth_output/"$samplename"_output.pdf \
 	/home/dnanexus/in/subpanel_bed/"$subpanel_bed_name":"$subpanel_bed_prefix" \
-	/home/dnanexus/in/readcount_file/"$readcount_file_name" \
-	"$bam_and_QC_command"
+	/home/dnanexus/in/readcount_file/"$readcount_file_name" "$bam":"$samplename":0.01 $QC_file
+
 done
 
 # Upload results