Finalize

FinalizeToFile

description
Copies the given file to the specified bucket.

Inputs

Required

  • file (File, required); description: file to finalize; localization_optional: true
  • outdir (String, required): directory to which files should be uploaded

Optional

  • keyfile (File?): [optional] File used to key this finaliation. Finalization will not take place until the KeyFile exists. This can be used to force the finaliation to wait until a certain point in a workflow. NOTE: The latest WDL development spec includes the after keyword which will obviate this.
  • name (String?): name to set for uploaded file
  • runtime_attr_override (RuntimeAttr?)

Outputs

  • gcs_path (String)

FinalizeToDir

description
Copies the given file to the specified bucket.

Inputs

Required

  • files (Array[File], required); description: files to finalize; localization_optional: true
  • outdir (String, required): directory to which files should be uploaded

Optional

  • keyfile (File?): [optional] File used to key this finaliation. Finalization will not take place until the KeyFile exists. This can be used to force the finaliation to wait until a certain point in a workflow. NOTE: The latest WDL development spec includes the after keyword which will obviate this.
  • runtime_attr_override (RuntimeAttr?)

Outputs

  • gcs_dir (String)

FinalizeTarGzContents

description
Copies the contents of the given tar.gz file to the specified bucket.
author
Jonn Smith
email
jonn@broadinstitute.org

Inputs

Required

  • outdir (String, required): Google cloud path to the destination folder.
  • tar_gz_file (File, required): Gzipped tar file whose contents we'll copy.

Optional

  • keyfile (File?): [optional] File used to key this finaliation. Finalization will not take place until the KeyFile exists. This can be used to force the finaliation to wait until a certain point in a workflow. NOTE: The latest WDL development spec includes the after keyword which will obviate this.
  • runtime_attr_override (RuntimeAttr?): [optional] Additional runtime parameters.

Outputs

None

WriteCompletionFile

description
Write a file to the given directory indicating the run has completed.
author
Jonn Smith
email
jonn@broadinstitute.org

Inputs

Required

  • outdir (String, required): Google cloud path to the destination folder.

Optional

  • keyfile (File?): [optional] File used to key this finaliation. Finalization will not take place until the KeyFile exists. This can be used to force the finaliation to wait until a certain point in a workflow. NOTE: The latest WDL development spec includes the after keyword which will obviate this.

Outputs

None

CompressAndFinalize

description
Gzip a file and finalize

Inputs

Required

  • file (File, required): File to compress and finalize.
  • outdir (String, required): Google cloud path to the destination folder.

Optional

  • name (String?): [optional] Name of the file to write. If not specified, the name of the input file will be used.
  • runtime_attr_override (RuntimeAttr?): [optional] Additional runtime parameters.

Outputs

  • gcs_path (String)

FinalizeAndCompress

description
Gzip a bunch of files and finalize to the same 'folder'

Inputs

Required

  • files (Array[File], required): Files to compress and finalize.
  • outdir (String, required): Google cloud path to the destination folder.
  • prefix (String, required): [optional] Prefix to add to the output files.

Optional

  • runtime_attr_override (RuntimeAttr?): [optional] Additional runtime parameters.

Outputs

  • gcs_path (String)

WriteNamedFile

description
Write a file to the given directory with the given name.
author
Jonn Smith
email
jonn@broadinstitute.org

Inputs

Required

  • name (String, required): Name of the file to write.
  • outdir (String, required): Google cloud path to the destination folder.

Optional

  • keyfile (File?): [optional] File used to key this finaliation. Finalization will not take place until the KeyFile exists. This can be used to force the finaliation to wait until a certain point in a workflow. NOTE: The latest WDL development spec includes the after keyword which will obviate this.

Outputs

None