Merge pull request #12 from mskcc/release_v1.1.0

Release v1.1.0

container/build.sh

@@ -3,4 +3,4 @@
 [ -e report ] && rm -rf report
 mkdir report
 cp -r ../* report/
-docker build -t "mskcc/argos_report:1.0.8" .
+docker build -t "mskcc/argos_report:1.1.0" .

cwl/project_level_report.cwl

@@ -10,12 +10,14 @@ requirements:
   StepInputExpressionRequirement: {}
   InlineJavascriptRequirement: {}
   DockerRequirement:
-    dockerPull: mskcc/argos_report:1.0.8
+    dockerPull: mskcc/argos_report:1.1.0
 
 inputs:
   request_id:
     type: string
-  sample_ids:
+  normal_ids:
+    type: string[]
+  tumor_ids:
     type: string[]
   portal_dir:
     type: Directory
@@ -29,12 +31,13 @@ steps:
     run: report.cwl
     in:
       request_id: request_id
-      sample_id: sample_ids
+      normal_id: normal_ids
+      tumor_id: tumor_ids
       portal_dir: portal_dir
       analysis_dir: analysis_dir
       oncokb_file: oncokb_file
 
-    scatter: sample_id
+    scatter: [normal_id,tumor_id]
     scatterMethod: dotproduct
     out: [output_file]
 

cwl/report.cwl

@@ -5,19 +5,24 @@ class: CommandLineTool
 baseCommand: [ "compile_sample_level.R" ]
 requirements:
   DockerRequirement:
-    dockerPull: mskcc/argos_report:1.0.8
+    dockerPull: mskcc/argos_report:1.1.0
 
 inputs:
   request_id:
     type: string
     inputBinding:
       position: 1
       prefix: '--request_id'
-  sample_id:
+  normal_id:
     type: string
     inputBinding:
       position: 2
-      prefix: '--sample_id'
+      prefix: '--normal_id'
+  tumor_id:
+    type: string
+    inputBinding:
+      position: 2
+      prefix: '--tumor_id'
   portal_dir:
     type: Directory
     inputBinding:

report/compile_sample_level.R

@@ -7,13 +7,14 @@ suppressPackageStartupMessages({
     library("argparse")
 })
 
-VERSION="1.0.3"
+VERSION="1.1.0"
 default_output_dir <- normalizePath(getwd())
 
 # start arg parser
 parser <- ArgumentParser()
 parser$add_argument("--request_id", help="Request id")
-parser$add_argument("--sample_id", help="Sample id")
+parser$add_argument("--normal_id", help="Normal sample id")
+parser$add_argument("--tumor_id", help="Tumor sample id")
 parser$add_argument("--analysis_dir", help="analysis_dir path")
 parser$add_argument("--portal_dir", help="portal_dir path")
 parser$add_argument("--oncokb_file", help="oncokb file path")
@@ -25,29 +26,16 @@ parser$add_argument("--output_dir", default=default_output_dir, help="Output dir
 
 args <- parser$parse_args()
 
-#temporary solution to get normal id. if a sample has zero mutations Goliath code can not identify the normal id causeing the report to fail
-#ideal solution would be getting the normal id and matching type (matched or POOLED) from the input but that requires the input.json to be updated
-#until we get the change in the operator to create the input.json as needed, we place a temporary solution.
-
-sample_pairing_file <- read_tsv(
-            file.path(args$portal_dir,"../sample_pairing.txt"),
-            col_names = c("Normal", "Tumor"),
-            progress=F
-            )
-
-args$tumor_id <- args$sample_id
-args$normal_id  <- sample_pairing_file[sample_pairing_file$Tumor == args$tumor_id, ]$Normal
-
-output_file_name=paste0("rpt_",args$request_id,"-",args$tumor_id,"__",VERSION,".html")
+output_file_name=paste0("rpt_",args$request_id,"-",args$normal_id,"__",args$tumor_id,"__",VERSION,".html")
 
 # compile the HTML report
 rmarkdown::render(
     input = "/usr/report/report_sample_level.Rmd",
     params = list(
         analysis_dir = args$analysis_dir,
         portal_dir = args$portal_dir,
-        tumor_id = args$tumor_id,
         normal_id = args$normal_id,
+        tumor_id = args$tumor_id,
         oncokb_file = args$oncokb_file
         # geneAnnotation_path = args$geneAnnotation_path,