Continue processing even if one process is crashing

courtois-neuromod / anat-processing

Pipeline to process anatomical data, including microstructure metrics from DWI and MT data

MIT License

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Closed jcohenadad closed 2 years ago

jcohenadad commented 3 years ago

Because of https://github.com/courtois-neuromod/anat-processing/issues/17, every time i run the pipeline it eventually crashes, which makes the addition of processes difficult: i cannot test them because the pipeline crashes before...

@agahkarakuzu is there a way to ignore crashes of a process/subject?

jcohenadad commented 3 years ago

for now my workaround is to rename the problematic subject as "_sub-06_ses-002_rec-dis2d_bp-cspine_T2w.nii.gz" so it is ignored...

agahkarakuzu commented 3 years ago

@jcohenadad you can see the error handling strategies here.

errorStrategy 'ignore'

Adding this directive to the process description (i.e. in a module) could achieve that.

agahkarakuzu commented 2 years ago

SCT is no longer using Nextflow, closing the issue.