Prepare a Submission

Start from the workflow's own declarations instead of a blank inputs file, and find out whether a run will work before spending time and money on it.

Scaffold

Generate an inputs template from the WDL, with types and documentation
Preflight

Check server, WDL, inputs and file paths before submitting
Automatic

submit runs the checks for you

The flow

pumbaa workflow scaffold  -w main.wdl -o inputs.json   # 1. generate
# ... fill in the placeholders ...
pumbaa workflow preflight -w main.wdl -i inputs.json   # 2. check
pumbaa workflow submit    -w main.wdl -i inputs.json   # 3. run (checks again)

Scaffold

pumbaa workflow scaffold --workflow FILE [OPTIONS]

Alias: pumbaa wf template

Flag	Alias	Description
`--workflow`	`-w`	WDL workflow file
`--output`	`-o`	Write to this file instead of stdout
`--all`		Include optional inputs, with their defaults
`--force`		Overwrite an existing output file

Required inputs come first, each with a placeholder carrying its type and — when the WDL documents it in parameter_meta — its description:

{
  "AlignReads.reads_fastq": "<FILL: File — Sequencing reads in FASTQ format>",
  "AlignReads.reference_files": "<FILL: Array[File]+ — Reference genome and its index files>",
  "AlignReads.sample_name": "<FILL: String — Identifier used to name outputs>"
}

Optional inputs are left out by default, so the file is minimal and ready to submit once filled. Add --all to include them with their default values.

With --output, the command also prints every input — including the optional ones — and the next steps:

✓ Wrote inputs.json for workflow AlignReads

 INPUT                       TYPE          REQUIRED  DEFAULT  DESCRIPTION
 AlignReads.reads_fastq      File          yes                Sequencing reads in FASTQ format
 AlignReads.reference_files  Array[File]+  yes                Reference genome and its index files
 AlignReads.sample_name      String        yes                Identifier used to name outputs
 AlignReads.threads          Int           no        4
 AlignReads.skip_qc          Boolean       no        false

Piping

Without --output only the JSON is printed, so pumbaa workflow scaffold -w main.wdl > inputs.json works.

Preflight

pumbaa workflow preflight --workflow FILE [OPTIONS]

Alias: pumbaa wf check

Flag	Alias	Description
`--workflow`	`-w`	WDL workflow file
`--inputs`	`-i`	Inputs JSON file
`--dependencies`	`-d`	Imports ZIP — checks that every import resolves
`--skip-paths`		Do not check that input files exist
`--skip-server`		Do not check that Cromwell is reachable

Preflight — workflow AlignReads
─────────────────────────────────────────
  ✓ Cromwell server  reachable
  ✓ WDL syntax       workflow AlignReads
  ⚠ Inputs           worth a look
      ⚠ AlignReads.threads: is the quoted number "8" where Int is expected
      ⚠ AlignReads.sampleName: not declared by this workflow — check for a typo
  ✗ Input files      missing files
      ✗ AlignReads.reference_files[1]: file does not exist: gs://bucket/ref.fai

✗ 1 problem(s) must be fixed before this run can start (2 warning(s) too)

The command exits non-zero when there are errors, so it can gate a script or CI job.

What is checked

Check	Blocks?	Notes
Cromwell reachable		Skipped with `--skip-server`
WDL parses		A parse failure is only a warning — Cromwell is the authority
Required inputs present
Placeholders replaced		Catches "scaffolded and submitted unedited"
Types match declarations		Only clear mismatches; coercible values warn instead
Keys declared by the workflow		Usually a typo, so a warning
`File` inputs exist		Missing is an error; unverifiable (no credentials) is only a warning
Imports resolve in the ZIP		Only when `-d` is given; checks the whole import tree, including transitive imports

Missing vs. unverifiable

If a path cannot be checked — no local cloud credentials, for instance — preflight warns instead of blocking: Cromwell may well have access this machine does not.

Submit runs it for you

pumbaa workflow submit runs the same checks before sending anything, so a broken submission fails in seconds instead of minutes. It always reports the outcome, so you can see the checks happened:

✓ Preflight passed.
✓ Workflow submitted successfully!

When there are non-blocking warnings, the full checklist is shown before the submission proceeds; when there are errors, nothing is submitted:

✗ 1 problem(s) must be fixed before this run can start

ℹ Nothing was submitted. Fix the problems above, or use --skip-preflight to submit anyway.

The server check is skipped there (submitting contacts the server anyway). Use --skip-preflight to bypass the checks entirely (it prints Preflight skipped. so the bypass is explicit).