diff --git a/README.Rmd b/README.Rmd index 176b29c..676c6b4 100644 --- a/README.Rmd +++ b/README.Rmd @@ -72,7 +72,7 @@ thisJob <- cromwell_submit_batch(WDL = "myworkflow.wdl", Return a data frame of all jobs run in the past number of days (uses your database) ```r -jobs <- cromwell_jobs(days = 2) +cromwell_jobs(days = 2) ``` Return a data frame (one line if you only submit one workflow id) containing workflow level metadata @@ -90,13 +90,16 @@ w$status Return a data frame containing all call level metadata ```r -c <- cromwell_call(thisOne) +df <- cromwell_call(thisOne) ``` Handy set of dplyr commands to tell you about how the various calls are doing ```r -c %>% group_by(callName, executionStatus) %>% summarize(status = n()) %>% arrange(executionStatus) +df %>% + group_by(callName, executionStatus) %>% + summarize(status = n()) %>% + arrange(executionStatus) ``` Returns a data frame containing call level call caching metadata @@ -108,7 +111,9 @@ ca <- cromwell_cache(thisOne) Handy set of dplyr commands to tell you about what sort of call caching is happening ```r -ca %>% group_by(callCaching.hit, callName) %>% summarize(hits = n()) +ca %>% + group_by(callCaching.hit, callName) %>% + summarize(hits = n()) ``` Opens up a popup in your browser with a timing diagram in it. @@ -120,19 +125,19 @@ cromwell_timing(thisOne) Returns a data frame containing call level failure metadata ```r -f <- cromwell_failures(thisOne) +cromwell_failures(thisOne) ``` Will tell Cromwell to abort the current workflow - note this cannot be undone and it will take a while to stop all the jobs. ```r -abort <- cromwell_abort(thisOne) +cromwell_abort(thisOne) ``` When a workflow is done, request information about the workflow outputs. ```r -out <- cromwell_outputs(thisOne) +cromwell_outputs(thisOne) ``` ### Misc stuff @@ -140,5 +145,6 @@ out <- cromwell_outputs(thisOne) Ugly list of raw metadata should you need it for workflow troubleshooting ```r -cromwell_glob(thisOne); WTF[["failures"]] +wtf <- cromwell_glob(thisOne) +wtf[["failures"]] ``` diff --git a/README.md b/README.md index 922c285..4eb5c19 100644 --- a/README.md +++ b/README.md @@ -64,7 +64,7 @@ thisJob <- cromwell_submit_batch(WDL = "myworkflow.wdl", Return a data frame of all jobs run in the past number of days (uses your database) ```r -jobs <- cromwell_jobs(days = 2) +cromwell_jobs(days = 2) ``` Return a data frame (one line if you only submit one workflow id) containing workflow level metadata @@ -82,13 +82,16 @@ w$status Return a data frame containing all call level metadata ```r -c <- cromwell_call(thisOne) +df <- cromwell_call(thisOne) ``` Handy set of dplyr commands to tell you about how the various calls are doing ```r -c %>% group_by(callName, executionStatus) %>% summarize(status = n()) %>% arrange(executionStatus) +df %>% + group_by(callName, executionStatus) %>% + summarize(status = n()) %>% + arrange(executionStatus) ``` Returns a data frame containing call level call caching metadata @@ -100,7 +103,9 @@ ca <- cromwell_cache(thisOne) Handy set of dplyr commands to tell you about what sort of call caching is happening ```r -ca %>% group_by(callCaching.hit, callName) %>% summarize(hits = n()) +ca %>% + group_by(callCaching.hit, callName) %>% + summarize(hits = n()) ``` Opens up a popup in your browser with a timing diagram in it. @@ -112,19 +117,19 @@ cromwell_timing(thisOne) Returns a data frame containing call level failure metadata ```r -f <- cromwell_failures(thisOne) +cromwell_failures(thisOne) ``` Will tell Cromwell to abort the current workflow - note this cannot be undone and it will take a while to stop all the jobs. ```r -abort <- cromwell_abort(thisOne) +cromwell_abort(thisOne) ``` When a workflow is done, request information about the workflow outputs. ```r -out <- cromwell_outputs(thisOne) +cromwell_outputs(thisOne) ``` ### Misc stuff @@ -132,5 +137,6 @@ out <- cromwell_outputs(thisOne) Ugly list of raw metadata should you need it for workflow troubleshooting ```r -cromwell_glob(thisOne); WTF[["failures"]] +wtf <- cromwell_glob(thisOne) +wtf[["failures"]] ```