Detecting errors in data unstaging #5345
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…/out Signed-off-by: jorgee <[email protected]>
Signed-off-by: jorgee <[email protected]>
Signed-off-by: jorgee <[email protected]>
Signed-off-by: jorgee <[email protected]>
Signed-off-by: jorgee <[email protected]>
pditommaso
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Dec 1, 2024
modules/nextflow/src/main/resources/nextflow/executor/command-run.txt
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pditommaso
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modules/nextflow/src/main/resources/nextflow/executor/command-run.txt
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Signed-off-by: Paolo Di Tommaso <[email protected]>
Signed-off-by: jorgee <[email protected]>
Signed-off-by: jorgee <[email protected]>
Signed-off-by: jorgee <[email protected]>
Improve handling unstage outputs and controls
Signed-off-by: Paolo Di Tommaso <[email protected]>
pditommaso
reviewed
Dec 2, 2024
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| ## Capture possible errors. | ||
| ## Can be caused either by the task script, unstage script or after script if defined | ||
| local last_err=$? | ||
| ## capture the task error first or fallback to unstage error | ||
| local exit_status=${nxf_main_ret:=0} | ||
| [[ ${exit_status} -eq 0 && ${nxf_unstage_ret:=0} -ne 0 ]] && exit_status=${nxf_unstage_ret:=0} | ||
| [[ ${exit_status} -eq 0 && ${last_err} -ne 0 ]] && exit_status=${last_err} |
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This is still very hard to decode, it would be nice to be more verbose about the different of last_err vs nxf_main_ret vs nxf_unstage_ret and the general logic.
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Ok reported as separate issue
pditommaso
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Dec 2, 2024
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Signed-off-by: jorgee <[email protected]> Signed-off-by: Paolo Di Tommaso <[email protected]> Co-authored-by: Paolo Di Tommaso <[email protected]> Signed-off-by: Christopher Hakkaart <[email protected]>
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close #3711