Merge pull request #3 from mskcc/dev_oncokb_file

Dev oncokb file

container/build.sh

@@ -3,4 +3,4 @@
 [ -e report ] && rm -rf report
 mkdir report
 cp -r ../* report/
-docker build -t "mskcc/argos_report:1.0.1" .
+docker build -t "mskcc/argos_report:1.0.3" .

cwl/project_level_report.cwl

@@ -0,0 +1,48 @@
+#!/usr/bin/env cwl-runner
+
+# concatenate tables; keep the header from the first file, then all lines minus header from all files
+#  strip the header comments that start with '#'
+cwlVersion: v1.0
+class: Workflow
+
+requirements:
+  ScatterFeatureRequirement: {}
+  StepInputExpressionRequirement: {}
+  InlineJavascriptRequirement: {}
+  DockerRequirement:
+    dockerPull: mskcc/argos_report:1.0.3
+
+inputs:
+  request_id:
+    type: string
+  sample_ids:
+    type: string[]
+  portal_dir:
+    type: Directory
+  analysis_dir:
+    type: Directory
+  oncokb_file:
+    type: File
+
+steps:
+  generate_project_report:
+    run: report.cwl
+    in:
+      request_id: request_id
+      sample_id: sample_ids
+      portal_dir: portal_dir
+      analysis_dir: analysis_dir
+      oncokb_file: oncokb_file
+
+    scatter: sample_id
+    scatterMethod: dotproduct
+    out: [output_file]
+
+
+outputs:
+  output_file:
+    type: File[]
+    outputSource: generate_project_report/output_file
+
+
+

cwl/report.cwl

@@ -5,7 +5,7 @@ class: CommandLineTool
 baseCommand: [ "compile_sample_level.R" ]
 requirements:
   DockerRequirement:
-    dockerPull: mskcc/argos_report:1.0.1
+    dockerPull: mskcc/argos_report:1.0.3
 
 inputs:
   request_id:
@@ -28,7 +28,11 @@ inputs:
     inputBinding:
       position: 4
       prefix: '--analysis_dir'
-
+  oncokb_file:
+      type: File
+      inputBinding:
+        position: 5
+        prefix: '--oncokb_file'
 
 
 outputs:

report/compile_sample_level.R

@@ -11,6 +11,7 @@ parser$add_argument("--request_id", help="Request id")
 parser$add_argument("--sample_id", help="Sample id")
 parser$add_argument("--analysis_dir", help="analysis_dir path")
 parser$add_argument("--portal_dir", help="portal_dir path")
+parser$add_argument("--oncokb_file", help="oncokb file path")
 parser$add_argument("--output_dir", default=default_output_dir, help="Output dirname")
 
 
@@ -27,7 +28,8 @@ rmarkdown::render(
     params = list(
         analysis_dir = args$analysis_dir,
         portal_dir = args$portal_dir,
-        sample_id=args$sample_id
+        sample_id = args$sample_id,
+        oncokb_file = args$oncokb_file
         # geneAnnotation_path = args$geneAnnotation_path,
 
     ),

report/report_sample_level.Rmd

@@ -14,13 +14,14 @@ params:
   analysis_dir : "~/Work/mutation_report_sample_level/data/argos/08390_R/1.1.2/20230208_22_12_784560/analysis/"
   portal_dir : "~/Work/mutation_report_sample_level/data/argos/08390_R/1.1.2/20230208_22_12_784560/portal/"
   sample_id : "s_C_8XFJMJ_P001_d01"
+  oncokb_file: "dummy"
 ---
 
 ```{r loadData, echo=FALSE, include=FALSE}
 
 
 source("load_data.R", local=knitr::knit_global())
-inputs <- list(analysis_dir = params$analysis_dir, portal_dir = params$portal_dir)
+inputs <- list(analysis_dir = params$analysis_dir, portal_dir = params$portal_dir, oncokb_file = params$oncokb_file)
 data=load_data(params$sample_id, inputs)
 ```