Merge pull request #10 from mskcc/dev_sv_match_status_from_normal_id

Dev sv match status from normal
mskcc · Jul 22, 2024 · 1d05a7a · 1d05a7a
2 parents 3692b68 + c927f0d
commit 1d05a7a
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Showing 6 changed files with 32 additions and 21 deletions.
diff --git a/Goliath b/Goliath
diff --git a/container/build.sh b/container/build.sh
@@ -3,4 +3,4 @@
 [ -e report ] && rm -rf report
 mkdir report
 cp -r ../* report/
-docker build -t "mskcc/argos_report:1.0.6" .
+docker build -t "mskcc/argos_report:1.0.7" .
diff --git a/cwl/project_level_report.cwl b/cwl/project_level_report.cwl
@@ -10,12 +10,14 @@ requirements:
   StepInputExpressionRequirement: {}
   InlineJavascriptRequirement: {}
   DockerRequirement:
-    dockerPull: mskcc/argos_report:1.0.6
+    dockerPull: mskcc/argos_report:1.0.7
 
 inputs:
   request_id:
     type: string
-  sample_ids:
+  tumor_ids:
+    type: string[]
+  normal_ids:
     type: string[]
   portal_dir:
     type: Directory
@@ -29,12 +31,13 @@ steps:
     run: report.cwl
     in:
       request_id: request_id
-      sample_id: sample_ids
+      tumor_id: tumor_ids
+      normal_id: normal_ids
       portal_dir: portal_dir
       analysis_dir: analysis_dir
       oncokb_file: oncokb_file
 
-    scatter: sample_id
+    scatter: [tumor_id, normal_id]
     scatterMethod: dotproduct
     out: [output_file]
 

diff --git a/cwl/report.cwl b/cwl/report.cwl
@@ -5,33 +5,38 @@ class: CommandLineTool
 baseCommand: [ "compile_sample_level.R" ]
 requirements:
   DockerRequirement:
-    dockerPull: mskcc/argos_report:1.0.6
+    dockerPull: mskcc/argos_report:1.0.7
 
 inputs:
   request_id:
     type: string
     inputBinding:
       position: 1
       prefix: '--request_id'
-  sample_id:
+  tumor_id:
     type: string
     inputBinding:
       position: 2
-      prefix: '--sample_id'
+      prefix: '--tumor_id'
+  normal_id:
+    type: string
+    inputBinding:
+      position: 3
+      prefix: '--normal_id'
   portal_dir:
     type: Directory
     inputBinding:
-      position: 3
+      position: 4
       prefix: '--portal_dir'
   analysis_dir:
     type: Directory
     inputBinding:
-      position: 4
+      position: 5
       prefix: '--analysis_dir'
   oncokb_file:
       type: File
       inputBinding:
-        position: 5
+        position: 6
         prefix: '--oncokb_file'
 
 

diff --git a/report/compile_sample_level.R b/report/compile_sample_level.R
@@ -2,13 +2,14 @@
 # script to compile report from pipeline data
 library("argparse")
 
-VERSION="1.0.1"
+VERSION="1.0.2"
 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$add_argument("--tumor_id", help="Tumor id")
+parser$add_argument("--normal_id", help="Normal id")
 parser$add_argument("--analysis_dir", help="analysis_dir path")
 parser$add_argument("--portal_dir", help="portal_dir path")
 parser$add_argument("--oncokb_file", help="oncokb file path")
@@ -20,15 +21,16 @@ parser$add_argument("--output_dir", default=default_output_dir, help="Output dir
 
 args <- parser$parse_args()
 
-output_file_name=paste0("rpt_",args$request_id,"-",args$sample_id,"__",VERSION,".html")
+output_file_name=paste0("rpt_",args$request_id,"-",args$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,
-        sample_id = args$sample_id,
+        tumor_id = args$tumor_id,
+        normal_id = args$normal_id,
         oncokb_file = args$oncokb_file
         # geneAnnotation_path = args$geneAnnotation_path,
 

diff --git a/report/report_sample_level.Rmd b/report/report_sample_level.Rmd
@@ -11,18 +11,19 @@ always_allow_html: true
 self_contained: true
 
 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"
+  analysis_dir : "/Users/vurals/Work/mutation_report/mutation_report_sample_level_v11_zero_mutations_case/15450_B/analysis/"
+  portal_dir : "/Users/vurals/Work/mutation_report/mutation_report_sample_level_v11_zero_mutations_case/15450_B/portal/"
+  tumor_id : "s_C_WA4R58_T003_d03"
+  normal_id : "s_C_WA4R58_N002_d02"
   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, oncokb_file = params$oncokb_file)
-data=load_data(params$sample_id, inputs)
+inputs <- list(tumor_id = params$tumor_id, normal_id = params$normal_id, analysis_dir = params$analysis_dir, portal_dir = params$portal_dir, oncokb_file = params$oncokb_file)
+data=load_data(params$tumor_id, params$normal_id, inputs)
 ```