View source: R/avworkflow_configuration.R
avworkflows | R Documentation |
avworkflows()
returns a tibble summarizing available
workflows.
avworkflow_jobs()
returns a tibble summarizing
submitted workflow jobs for a namespace and name.
avworkflow_files()
returns a tibble containing
information and file paths to workflow outputs.
avworkflow_localize()
creates or synchronizes a
local copy of files with files stored in the workspace bucket
and produced by the workflow.
avworkflow_run()
runs the workflow of the configuration.
avworkflow_stop()
stops the most recently submitted workflow
jub from running.
avworkflows(namespace = avworkspace_namespace(), name = avworkspace_name()) avworkflow_jobs(namespace = avworkspace_namespace(), name = avworkspace_name()) avworkflow_files(submissionId = NULL, bucket = avbucket()) avworkflow_localize( submissionId = NULL, destination = NULL, type = c("control", "output", "all"), bucket = avbucket(), dry = TRUE ) avworkflow_run( config, entityName, entityType = config$rootEntityType, deleteIntermediateOutputFiles = FALSE, useCallCache = TRUE, namespace = avworkspace_namespace(), name = avworkspace_name(), dry = TRUE ) avworkflow_stop( submissionId = NULL, namespace = avworkspace_namespace(), name = avworkspace_name(), dry = TRUE )
namespace |
character(1) AnVIL workspace namespace as returned
by, e.g., |
name |
character(1) AnVIL workspace name as returned by, eg.,
|
submissionId |
a character() of workflow submission ids, or a
tibble with column |
bucket |
character(1) name of the google bucket in which the
workflow products are available, as |
destination |
character(1) file path to the location where
files will be synchronized. For directories in the current
working directory, be sure to prepend with |
type |
character(1) copy |
dry |
logical(1) when |
config |
a |
entityName |
character(1) name of the set of samples to be used when running the workflow. |
entityType |
character(1) type of root entity used for the workflow. |
deleteIntermediateOutputFiles |
logical(1) whether or not to delete intermediate output files when the workflow completes. |
useCallCache |
logical(1) whether or not to read from cache for this submission. |
For avworkflow_files()
, the submissionId
is the
identifier associated with the workflow job, and is present in
the return value of avworkflow_jobs()
; the example
illustrates how the first row of avworkflow_jobs()
(i.e., the
most recenltly completed workflow) can be used as input to
avworkflow_files()
. When submissionId
is not provided, the
return value is for the most recently submitted workflow of the
namespace and name of avworkspace()
.
avworkflow_localize()
. type = "control"
files
summarize workflow progress; they can be numerous but are
frequently small and quickly syncronized. type = "output"
files are the output products of the workflow stored in the
workspace bucket. Depending on the workflow, outputs may be
large, e.g., aligned reads in bam files. See gsutil_cp()
to
copy individual files from the bucket to the local drive.
avworkflow_localize()
treats submissionId=
in the same way as
avworkflow_files()
: when missing, files from the most recent
workflow job are candidates for localization.
avworkflows()
returns a tibble. Each workflow is in a
'namespace' and has a 'name', as illustrated in the
example. Columns are
name: workflow name.
namespace: workflow namespace (often the same as the workspace namespace).
rootEntityType: name of the avtable()
used to retrieve inputs.
methodRepoMethod.methodUri: source of the method, e.g., a dockstore URI.
methodRepoMethod.sourceRepo: source repository, e.g., dockstore.
methodRepoMethod.methodPath: path to method, e.g., a dockerstore method might reference a github repository.
methodRepoMethod.methodVersion: the version of the method, e.g., 'main' branch of a github repository.
avworkflow_jobs()
returns a tibble, sorted by
submissionDate
, with columns
submissionId character() job identifier from the workflow runner.
submitter character() AnVIL user id of individual submitting the job.
submissionDate POSIXct() date (in local time zone) of job submission.
status character() job status, with values 'Accepted' 'Evaluating' 'Submitting' 'Submitted' 'Aborting' 'Aborted' 'Done'
succeeded integer() number of workflows succeeding.
failed integer() number of workflows failing.
avworkflow_files()
returns a tibble with columns
file: character() 'base name' of the file in the bucket.
workflow: character() name of the workflow the file is associated with.
task: character() name of the task in the workflow that generated the file.
path: charcter() full path to the file in the google bucket.
avworkflow_localize()
prints a message indicating the
number of files that are (if dry = FALSE
) or would be
localized. If no files require localization (i.e., local files
are not older than the bucket files), then no files are
localized. avworkflow_localize()
returns a tibble of file
name and bucket path of files to be synchronized.
avworkflow_run()
returns config
, invisibly.
avworkflow_stop()
returns NULL, invisibly.
if (gcloud_exists() && nzchar(avworkspace_name())) ## from within AnVIL avworkflows() %>% select(namespace, name) if (gcloud_exists() && nzchar(avworkspace_name())) ## from within AnVIL avworkflow_jobs() if (gcloud_exists() && nzchar(avworkspace_name())) { ## e.g., from within AnVIL avworkflow_jobs() %>% ## select most recent workflow head(1) %>% ## find paths to output and log files on the bucket avworkflow_files() } if (gcloud_exists() && nzchar(avworkspace_name())) { avworkflow_localize(dry = TRUE) } ## Not run: entityName <- avtable("participant_set") |> pull(participant_set_id) |> head(1) avworkflow_run(new_config, entityName) ## End(Not run) ## Not run: avworkflow_stop() ## End(Not run)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.