update docs for release

getwilds · Oct 5, 2021 · 1f3f40f · 1f3f40f
1 parent 1881b06
commit 1f3f40f
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,26 +1,26 @@
 Package: fh.wdlR
 Title: Convenience Tools for Managing WDL Workflows via Cromwell
-Version: 1.0.1
+Version: 1.1.0
 Authors@R: 
     person(given = "Amy",
            family = "Paguirigan",
            role = c("aut", "cre"),
            email = "[email protected]",
            comment = c(ORCID = "0000-0002-6819-9736"))
-Description: A repo containing a basic R package for using Cromwell with WDL workflows at Fred Hutch via R.
+Description: A repo containing a basic R package for using Cromwell with WDL workflows via R.
 Imports:
     httr,
     jsonlite,
     magrittr,
     dplyr,
     purrr,
-    paws,
     tidyr,
-    ssh,
-    lubridate
+    lubridate,
+    paws,
+    ssh
 License: GPL-3
 Depends: R (>= 3.6.0)
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 Encoding: UTF-8
 LazyData: true
diff --git a/R/cromwellCall.R b/R/cromwellCall.R
@@ -97,7 +97,7 @@ cromwellCall <- function(workflow_id, cromURL = Sys.getenv("CROMWELLURL", unset
         if ("end" %in% colnames(justSubCalls) == T) {
           # and if end is present
           justSubCalls$end <-lubridate::with_tz(lubridate::ymd_hms(justSubCalls$end), tzone = "US/Pacific")
-          justSubCalls <- justSubCalls %>% mutate(callDuration = ifelse(is.na(justSubCalls$end) == T,
+          justSubCalls <- justSubCalls %>% dplyr::mutate(callDuration = ifelse(is.na(justSubCalls$end) == T,
                                                                         round(difftime(lubridate::now(tz = "US/Pacific"), justSubCalls$start, units = "mins"),3),
                                                                         round(difftime(justSubCalls$end, justSubCalls$start, units = "mins"), 3)))
         } else {
@@ -161,7 +161,7 @@ cromwellCall <- function(workflow_id, cromURL = Sys.getenv("CROMWELLURL", unset
         if ("end" %in% colnames(justCalls) == T) {
           # and if end is present
           justCalls$end <-lubridate::with_tz(lubridate::ymd_hms(justCalls$end), tzone = "US/Pacific")
-          justCalls <- justCalls %>% mutate(callDuration = ifelse(is.na(justCalls$end) == T,
+          justCalls <- justCalls %>% dplyr::mutate(callDuration = ifelse(is.na(justCalls$end) == T,
                  round(difftime(lubridate::now(tz = "US/Pacific"), justCalls$start, units = "mins"),3),
                  round(difftime(justCalls$end, justCalls$start, units = "mins"), 3)))
         } else {