Avoid printing in find_executables_remote [skip ci]

R/required_cols.R

@@ -5,6 +5,7 @@
 #' @param dataset_type Dataset type ("GWAS" or "QTL"). 
 #' @param for_all Columns required for all methods.
 #' @param add_versions Add software versions for each method.
+#' @param add_sources Add source code URLs for each method.
 #' @param add_citations Add citations for each method.
 #' @param add_executables Add path to executables for each method.
 #' @param verbose Print messages.
@@ -15,6 +16,7 @@
 required_cols <- function(dataset_type = "GWAS",
                           for_all = c("SNP","CHR","POS","Effect","StdErr"),
                           add_versions = FALSE,
+                          add_sources = TRUE,
                           add_citations = TRUE,
                           add_executables = FALSE,
                           verbose = TRUE){
@@ -42,22 +44,11 @@ required_cols <- function(dataset_type = "GWAS",
                            PAINTOR=c("MAF"),
                            COJO_stepwise=c("Freq","P","N"),
                            COJO_conditional=c("Freq","P","N"),
-                           COJO_joint=c("Freq","P","N")) # check these
-    #### Add GitHub repos ####
-    url_dict <- list(ABF="https://github.com/chr1swallace/coloc",
-                     FINEMAP="http://www.christianbenner.com/",
-                     SUSIE="https://github.com/stephenslab/susieR",
-                     POLYFUN_SUSIE="https://github.com/omerwe/polyfun",
-                     POLYFUN_FINEMAP="https://github.com/omerwe/polyfun",
-                     PAINTOR="https://github.com/gkichaev/PAINTOR_V3.0",
-                     COJO_stepwise="https://github.com/jianyangqt/gcta",
-                     COJO_conditional="https://github.com/jianyangqt/gcta",
-                     COJO_joint="https://github.com/jianyangqt/gcta") 
+                           COJO_joint=c("Freq","P","N")) # check these 
 
     d <- data.table::data.table(method=names(required_dict),
                                 required=required_dict)
     d$suggested <- suggested_dict[d$method]
-    d$url <- url_dict[d$method]
     #### Extract software versions ####
     if(isTRUE(add_versions)){
         messager("Gathering method versions.",v=verbose)
@@ -74,9 +65,23 @@ required_cols <- function(dataset_type = "GWAS",
                               COJO_joint=cojo_version) 
         d$version <- unlist(lapply(versions_dict[d$method],as.character))
     } 
+    #### Add GitHub repos ####
+    if(isTRUE(add_sources)){
+        messager("Gathering method sources.",v=verbose)
+        source_dict <- list(ABF="https://github.com/chr1swallace/coloc",
+                            FINEMAP="http://www.christianbenner.com/",
+                            SUSIE="https://github.com/stephenslab/susieR",
+                            POLYFUN_SUSIE="https://github.com/omerwe/polyfun",
+                            POLYFUN_FINEMAP="https://github.com/omerwe/polyfun",
+                            PAINTOR="https://github.com/gkichaev/PAINTOR_V3.0",
+                            COJO_stepwise="https://github.com/jianyangqt/gcta",
+                            COJO_conditional="https://github.com/jianyangqt/gcta",
+                            COJO_joint="https://github.com/jianyangqt/gcta")  
+        d$source <- source_dict[d$method]
+    }
     #### Extract executable paths ####
     if(isTRUE(add_executables)){
-        messager("Gathering method executables",v=verbose)
+        messager("Gathering method executables.",v=verbose)
         finemap <- FINEMAP_find_executable(verbose = FALSE)
         polyfun <- POLYFUN_find_folder()
         paintor <- PAINTOR_find_executable()
@@ -94,7 +99,7 @@ required_cols <- function(dataset_type = "GWAS",
     } 
     #### Add citations ####
     if(isTRUE(add_citations)){
-        messager("Gathering method citations",v=verbose)
+        messager("Gathering method citations.",v=verbose)
         citations_dict <- list(
             ABF="https://doi.org/10.1086%2F519024",
             FINEMAP="https://doi.org/10.1093%2Fbioinformatics%2Fbtw018",