add merge and decode as individual step in nextflow

main.nf

@@ -95,6 +95,9 @@ workflow BPC_PIPELINE {
    if (params.step == "update_potential_phi_fields_table") {
     update_potential_phi_fields_table(ch_comment, params.production)
     // validate_data.out.view()
+   } else if (params.step == "merge_and_uncode_rca_uploads"){
+    merge_and_uncode_rca_uploads("default", ch_cohort, params.production)
+   }
    } else if (params.step == "genie_bpc_pipeline"){
     update_potential_phi_fields_table(ch_comment, params.production)
     run_quac_upload_report_error(update_potential_phi_fields_table.out, ch_cohort)

modules/merge_and_uncode_rca_uploads.nf

@@ -19,7 +19,7 @@ process merge_and_uncode_rca_uploads {
    if (production) {
       """
       cd /usr/local/src/myscripts/
-      Rscript merge_and_uncode_rca_uploads.R -c $cohort -u -v
+      Rscript merge_and_uncode_rca_uploads.R -c $cohort -v --production
       """
    }
    else {

nextflow.config

@@ -53,6 +53,7 @@ profiles {
 		params {
 			// docker image parameters, see nextflow_schema.json for details
 			references_docker = "sagebionetworks/genie-bpc-pipeline-references"
+			uploads_docker = "sagebionetworks/genie-bpc-pipeline-uploads"
 		}
 	}
 }

nextflow_schema.json

@@ -57,6 +57,10 @@
                     "type": "string",
                     "description": "Name of docker to use in processes in scripts/references"
                 },
+                "uploads_docker":{
+                    "type": "string",
+                    "description": "Name of docker to use in processes in scripts/uploads"
+                },
                 "schema_ignore_params": {
                     "type": "string",
                     "description": "Put parameters to ignore for validation here separated by comma",

scripts/uploads/merge_and_uncode_rca_uploads.R

@@ -687,7 +687,7 @@ main <- function(){
                 help="Save output to Synapse"),
     make_option(c("-a", "--synapse_auth"), type = "character", default = NA,
                 help="Path to .synapseConfig file or Synapse PAT (default: normal synapse login behavior)"),
-    make_option(c("-p", "--production"), action="store_true", default = FALSE, 
+    make_option(c("--production"), action="store_true", default = FALSE, 
                 help="Whether to run in production mode or not (staging mode)."),
     make_option(c("-v", "--verbose"), action="store_true", default = FALSE, 
                 help="Print out verbose output on script progress")