avworkflow: Working with AnVIL Workflow submissions and file outputs
In AnVIL: Bioconductor on the AnVIL compute environment

Description Usage Arguments Details Value Examples

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.

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avworkflow_jobs(namespace = avworkspace_namespace(), name = avworkspace_name())

avworkflow_files(submissionId = NULL, bucket = avbucket())

`namespace`	character(1) AnVIL workspace namespace as returned by, e.g., `avworkspace_namespace()`
`name`	character(1) AnVIL workspace name as returned by, eg., `avworkspace_name()`.
`submissionId`	a character() of workflow submission ids, or a tibble with column `submissionId`, or NULL / missing. See 'Details'.
`bucket`	character(1) name of the google bucket in which the workflow products are available, as `gs://...`. Usually the bucket of the active workspace, returned by `avbucket()`.

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_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.
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.

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()
}