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Add workaround for compatibility with WDL workflows that expect the user to have access to task-level outputs #5093

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adamnovak opened this issue Sep 17, 2024 · 1 comment · Fixed by #5096
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Add workaround for compatibility with WDL workflows that expect the user to have access to task-level outputs #5093

adamnovak opened this issue Sep 17, 2024 · 1 comment · Fixed by #5096
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adamnovak commented Sep 17, 2024 •
edited by unito-bot
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The ENCODE ATAC-seq workflow produces important files as task-level outputs. But since it has a workflow-level output section that does not include them, Toil discards them.

We should allow the user to override the WDL spec and preserve/export task outputs instead of or in addition to any workflow-level outputs, to support running this workflow and any others like it.

We probably need to touch here:

toil/src/toil/wdl/wdltoil.py

Lines 3394 to 3414 in 8faca0f

if self._workflow.outputs is None:
# The output section is not declared
# So get all task outputs and return that
# First get all task output names
output_set = set()
for call in self._workflow.body:
if isinstance(call, WDL.Tree.Call):
for type_binding in call.effective_outputs:
output_set.add(type_binding.name)
# Collect all bindings that are task outputs
output_bindings: WDL.Env.Bindings[WDL.Value.Base] = WDL.Env.Bindings()
for binding in unwrap(self._bindings):
if binding.name in output_set:
# The bindings will already be namespaced with the task namespaces
output_bindings = output_bindings.bind(binding.name, binding.value)
else:
# Output section is declared and is nonempty, so evaluate normally
# Combine the bindings from the previous job
with monkeypatch_coerce(standard_library):
output_bindings = evaluate_output_decls(self._workflow.outputs, unwrap(self._bindings), standard_library)

┆Issue is synchronized with this Jira Story
┆Issue Number: TOIL-1646
@adamnovak adamnovak added the wdl label Sep 17, 2024
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➤ Adam Novak commented:

We might want to have some magic to sniff out this particular workflow (or maybe anything with croo metadata) and turn this on by default, to annoy the fewest users.

This was referenced Sep 18, 2024
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Sniffing for and workaround for keeping output of croo workflows DataBiosphere/toil
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