Specify samples to include

README.md

@@ -1,4 +1,4 @@
-# dnanexus_ED_cnv_analysis_v1.3.0
+# dnanexus_ED_cnv_analysis_v1.3.1
 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.
@@ -19,6 +19,7 @@ For further details on the usage of the docker image please refer to https://git
 - Readcount file 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
+- Optional: list of comma separated samples if want to run a specific sample or a list of samples only. Use the sample name before the Pan number (e.g. NGS629_01_xxxxxx_NA12878_U_VCP2R208ViaGP08,NGS629_02_xxxxxx_NA12878_U_VCP2R208ViaGP08)
 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.
 
@@ -34,7 +35,7 @@ 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 
+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 -iincluded_samples=NGS629_01_xxxxxx_NA12878_U_VCP2R208ViaGP08,NGS629_02_xxxxxx_NA12878_U_VCP2R208ViaGP08
 ```
 # Debugging
 

dxapp.json

@@ -1,9 +1,9 @@
 {
-  "name": "ED_cnv_calling_v1.3.0",
-  "title": "ED_cnv_calling_v1.3.0",
-  "summary": "v1.3.0 - Performs CNV calling using ExomeDepth",
+  "name": "ED_cnv_calling_v1.3.1",
+  "title": "ED_cnv_calling_v1.3.1",
+  "summary": "v1.3.1 - Performs CNV calling using ExomeDepth",
   "properties": {
-    "github release": "v1.3.0"
+    "github release": "v1.3.1"
   },
   "dxapi": "1.0.0",
   "inputSpec": [
@@ -34,6 +34,13 @@
       "class": "file",
       "patterns": ["*.bed"],
       "optional": false
+    },
+    {
+      "name": "included_samples",
+      "label": "included samples",
+      "class": "string",
+      "optional": true,
+      "help": "comma separated sample name(s) to be included. Use the sample name before the Pan number"
     }
   ],
   "outputSpec": [

src/code.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-# exomedepth_cnv_analysis_v1.3.0
+# exomedepth_cnv_analysis_v1.3.1
 
 # 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
@@ -50,10 +50,16 @@ mark-section "download bams files and indexes"
 # split this into an array and loop through to download BAM and BAI files
 IFS=',' read -ra pannum_array <<<  $bamfile_pannumbers
 for panel in "${pannum_array[@]}"; do
-
-if [[ " ${pans_from_bams[*]} " =~ " ${panel} " ]]; then
-    # If requested pan number has matching bam files
+if [[ " ${pans_from_bams[*]} " =~ " ${panel} " ]] && [[ ! "$included_samples" ]]; then
+    # If requested pan number has matching bam files and included_samples is not provided
 	dx download "$project_name":output/*"$panel"*001.ba* --auth "$API_KEY"
+elif [[ " ${pans_from_bams[*]} " =~ " ${panel} " ]] && [[ "$included_samples" ]]; then
+    # If requested pan number has matching bam files and included_samples is provided
+	IFS=',' read -ra included_samples_array <<<  $included_samples
+	for sample in ${included_samples_array[@]}
+	do  
+	    dx download "$project_name":output/"$sample"*"$panel"*001.ba* --auth "$API_KEY"
+	done
 else
     echo "WARNING: No bam/bai files found for ${panel}"
 fi
@@ -114,7 +120,7 @@ echo "RDATA = " "$readcount_file_name"
 docker run -v /home/dnanexus:/home/dnanexus/ \
 	--rm  ${DOCKERIMAGENAME} \
 	exomeDepth.R \
-	'v1.3.0' \
+	'v1.3.1' \
 	/home/dnanexus/out/exomedepth_output/exomedepth_output/"$samplename"_output.pdf \
 	/home/dnanexus/in/subpanel_bed/"$subpanel_bed_name":"$subpanel_bed_prefix" \
 	/home/dnanexus/in/readcount_file/"$readcount_file_name" "$bam":"$samplename":0.01 $QC_file