Merge pull request #144 from Sage-Bionetworks/nf-clinical-release

[GEN-1503] Add nextflow workflow for clinical release

main.nf

@@ -76,14 +76,15 @@ include { run_quac_table_report } from './modules/run_quac_table_report'
 include { run_quac_comparison_report } from './modules/run_quac_comparison_report'
 include { create_masking_report } from './modules/create_masking_report'
 include { update_case_count_table } from './modules/update_case_count_table'
+include { run_clinical_release } from './modules/run_clinical_release'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     RUN WORKFLOW
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-workflow {
+workflow BPC_PIPELINE {
    ch_cohort = Channel.value(params.cohort)
    ch_comment = Channel.value(params.comment)
 
@@ -104,3 +105,7 @@ workflow {
     THE END
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
+
+workflow CLINICAL_RELEASE {
+    run_clinical_release('', params.cohort, params.production)
+}

modules/run_clinical_release.nf

@@ -0,0 +1,28 @@
+process run_clinical_release {
+
+   container 'sagebionetworks/genie-bpc-pipeline-clinical-release'
+   secret 'SYNAPSE_AUTH_TOKEN'
+   debug true
+
+   input:
+   val previous
+   val cohort
+   val production
+
+   output:
+   stdout
+
+   script:
+   if (production) {
+      """
+      cd /usr/local/src/myscripts/
+      Rscript create_release_files.R -c $cohort -v -s
+      """
+   }
+   else {
+      """
+      cd /usr/local/src/myscripts/
+      Rscript create_release_files.R -c $cohort -v
+      """
+   }
+}

nextflow.config

@@ -41,6 +41,10 @@ profiles {
 				memory = 32.GB
 				cpus = 8
 			}
+			withName: run_clinical_release {
+				memory = 32.GB
+				cpus = 8
+			}
 		}
 	}
 }

scripts/release/Dockerfile

@@ -0,0 +1,19 @@
+FROM rstudio/r-base:4.0-bullseye
+
+WORKDIR /usr/local/src/myscripts
+
+ENV RENV_VERSION 0.14.0
+# RUN rm /etc/apt/apt.conf.d/default
+RUN apt-get update -y && apt-get install -y dpkg-dev zlib1g-dev libssl-dev libffi-dev curl libcurl4-openssl-dev procps
+
+
+RUN R -e "install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))"
+RUN R -e "remotes::install_github('rstudio/renv@${RENV_VERSION}')"
+RUN R -e "remotes::install_version('synapser', version = '0.11.7', repos = c('http://ran.synapse.org', 'http://cran.fhcrc.org'))"
+
+ENV PYTHON /usr/local/lib/R/site-library/PythonEmbedInR/bin/python3.6
+
+
+COPY . .
+
+RUN R -e "renv::restore()"

scripts/release/create_release_files.R

@@ -27,10 +27,6 @@ option_list <- list(
               action="store_true", 
               default = FALSE,
               help="Copy release files from staging to release folder"),
-  make_option(c("-a", "--auth"), 
-              type = "character",
-              default = NA,
-              help="Synapse personal access token or path to .synapseConfig (default: normal synapse login behavior)"),
   make_option(c("-v", "--verbose"), 
               action="store_true", 
               default = FALSE,
@@ -41,7 +37,6 @@ opt <- parse_args(OptionParser(option_list=option_list))
 selected_cohort <- opt$cohort
 staging <- opt$staging
 release <- opt$release
-auth <- opt$auth
 verbose <- opt$verbose
 
 if (verbose) {
@@ -121,68 +116,10 @@ store_file <- function(var,
   }
 }
 
-#' Extract personal access token from .synapseConfig
-#' located at a custom path. 
-#' 
-#' @param path Path to .synapseConfig
-#' @return personal acccess token
-get_auth_token <- function(path) {
-
-  lines <- scan(path, what = "character", sep = "\t", quiet = T)
-  line <- grep(pattern = "^authtoken = ", x = lines, value = T)
-
-  token <- strsplit(line, split = ' ')[[1]][3]
-  return(token)
-}
-
-#' Override of synapser::synLogin() function to accept 
-#' custom path to .synapseConfig file or personal authentication
-#' token.  If no arguments are supplied, performs standard synLogin().
-#' 
-#' @param auth full path to .synapseConfig file or authentication token
-#' @param silent verbosity control on login
-#' @return TRUE for successful login; F otherwise
-synLogin <- function(auth = NA, silent = T) {
-
-  secret <- Sys.getenv("SCHEDULED_JOB_SECRETS")
-  if (secret != "") {
-    # Synapse token stored as secret in json string
-    syn = synapser::synLogin(silent = T, authToken = fromJSON(secret)$SYNAPSE_AUTH_TOKEN)
-  } else if (auth == "~/.synapseConfig" || is.na(auth)) {
-    # default Synapse behavior
-    syn <- synapser::synLogin(silent = silent)
-  } else {
-
-    # in case pat passed directly
-    token <- auth
-
-    # extract token from custom path to .synapseConfig
-    if (grepl(x = auth, pattern = "\\.synapseConfig$")) {
-      token = get_auth_token(auth)
-
-      if (is.na(token)) {
-        return(F)
-      }
-    }
-
-    # login with token
-    syn <- tryCatch({
-      synapser::synLogin(authToken = token, silent = silent)
-    }, error = function(cond) {
-      return(F)
-    })
-  }
-
-  # NULL returned indicates successful login
-  if (is.null(syn)) {
-    return(T)
-  }
-  return(F)
-}
 
 # synapse login ---------------
 
-status <- synLogin(auth = auth)
+synLogin()
 
 # read --------------------