From 72e979bad11a5c6b47b1e6c64d16c605a18c0edc Mon Sep 17 00:00:00 2001 From: Suleyman Vural Date: Thu, 18 Jul 2024 16:44:30 -0400 Subject: [PATCH 1/4] adding normal id as input --- report/compile_sample_level.R | 6 ++++-- report/report_sample_level.Rmd | 3 ++- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/report/compile_sample_level.R b/report/compile_sample_level.R index 5514fa2..4b62857 100755 --- a/report/compile_sample_level.R +++ b/report/compile_sample_level.R @@ -8,7 +8,8 @@ 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$add_argument("--oncokb_file", help="oncokb file path") @@ -28,7 +29,8 @@ rmarkdown::render( params = list( analysis_dir = args$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 index 6e9c282..345a2d9 100644 --- a/report/report_sample_level.Rmd +++ b/report/report_sample_level.Rmd @@ -13,7 +13,8 @@ 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" + tumor_id : "s_C_8XFJMJ_P001_d01" + normal_id : "s_C_ABCDEF_N001_d01" oncokb_file: "dummy" --- From 1f48278c5b168ff59800a12ad935f0b91d718fef Mon Sep 17 00:00:00 2001 From: Suleyman Vural Date: Mon, 22 Jul 2024 10:35:27 -0400 Subject: [PATCH 2/4] adding normal_id as an input --- report/compile_sample_level.R | 4 ++-- report/report_sample_level.Rmd | 12 ++++++------ 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/report/compile_sample_level.R b/report/compile_sample_level.R index 4b62857..c654656 100755 --- a/report/compile_sample_level.R +++ b/report/compile_sample_level.R @@ -2,7 +2,7 @@ # 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 @@ -21,7 +21,7 @@ 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( diff --git a/report/report_sample_level.Rmd b/report/report_sample_level.Rmd index 345a2d9..a6b7765 100644 --- a/report/report_sample_level.Rmd +++ b/report/report_sample_level.Rmd @@ -11,10 +11,10 @@ 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/" - tumor_id : "s_C_8XFJMJ_P001_d01" - normal_id : "s_C_ABCDEF_N001_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" --- @@ -22,8 +22,8 @@ params: 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) ``` From 5566a5a89fff698dfcca5232ff94716244824480 Mon Sep 17 00:00:00 2001 From: Suleyman Vural Date: Mon, 22 Jul 2024 12:25:36 -0400 Subject: [PATCH 3/4] adding normal_id as an input --- Goliath | 2 +- cwl/project_level_report.cwl | 11 +++++++---- cwl/report.cwl | 17 +++++++++++------ 3 files changed, 19 insertions(+), 11 deletions(-) diff --git a/Goliath b/Goliath index f6e3db8..5165842 160000 --- a/Goliath +++ b/Goliath @@ -1 +1 @@ -Subproject commit f6e3db8ff32e672762a4d032296776fa6754659f +Subproject commit 51658423297de5280d12a3e98af072e16657c7d8 diff --git a/cwl/project_level_report.cwl b/cwl/project_level_report.cwl index b320163..b5925ea 100644 --- 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:dev 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 index b50e0fd..317f15e 100644 --- a/cwl/report.cwl +++ b/cwl/report.cwl @@ -5,7 +5,7 @@ class: CommandLineTool baseCommand: [ "compile_sample_level.R" ] requirements: DockerRequirement: - dockerPull: mskcc/argos_report:1.0.6 + dockerPull: mskcc/argos_report:dev inputs: request_id: @@ -13,25 +13,30 @@ inputs: 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' From c927f0d9cd20ad20c697349b0f2c7fb9596bcbf1 Mon Sep 17 00:00:00 2001 From: svural Date: Mon, 22 Jul 2024 15:38:27 -0400 Subject: [PATCH 4/4] adding normal_id as an input --- container/build.sh | 2 +- cwl/project_level_report.cwl | 2 +- cwl/report.cwl | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/container/build.sh b/container/build.sh index 6821485..b337a7f 100755 --- 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 index b5925ea..64a61f0 100644 --- a/cwl/project_level_report.cwl +++ b/cwl/project_level_report.cwl @@ -10,7 +10,7 @@ requirements: StepInputExpressionRequirement: {} InlineJavascriptRequirement: {} DockerRequirement: - dockerPull: mskcc/argos_report:dev + dockerPull: mskcc/argos_report:1.0.7 inputs: request_id: diff --git a/cwl/report.cwl b/cwl/report.cwl index 317f15e..fb98d73 100644 --- a/cwl/report.cwl +++ b/cwl/report.cwl @@ -5,7 +5,7 @@ class: CommandLineTool baseCommand: [ "compile_sample_level.R" ] requirements: DockerRequirement: - dockerPull: mskcc/argos_report:dev + dockerPull: mskcc/argos_report:1.0.7 inputs: request_id: