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Fix staging and resume for typed record inputs with nested Path fields#7083

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stekaz wants to merge 1 commit intonextflow-io:masterfrom
stekaz:fix
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Fix staging and resume for typed record inputs with nested Path fields#7083
stekaz wants to merge 1 commit intonextflow-io:masterfrom
stekaz:fix

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@stekaz
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@stekaz stekaz commented Apr 28, 2026

Typed process inputs using record types with nested Path fields are (currently) not always handled like normal file inputs.

For example, given an input such as:

input:
sample: SampleRecord

where SampleRecord.path is a Path, the compiler should implicitly stage sample.path into the task work directory and rewrite references such as:

${resource.path}

to the process working directory, for example:

input.txt

But in some cases this does not happen. The compiler can miss the implicit file stager for nested Path fields. When that happens, task scripts either render the original source path instead of the staged task-local path, or the expected file could be missing from the working directory. And -resume could behave incorrectly.

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Is this related to #7032 ?

@stekaz stekaz force-pushed the fix branch 2 times, most recently from 8983f0d to 6e13a14 Compare April 29, 2026 12:35
Signed-off-by: Stephen Kazakoff <sh.kazakoff@gmail.com>
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stekaz commented Apr 29, 2026

Yes - I think they're both in the same problem area, but the failure modes are different. This PR fixes the input-side staging/localization (and resume) for typed records with nested Path fields. The other issue occurs when a record input is reused in an output record causing the downstream process to receive paths that are only valid in the upstream context.

@stekaz stekaz marked this pull request as ready for review April 29, 2026 14:09
@stekaz stekaz requested a review from a team as a code owner April 29, 2026 14:09
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2 participants