search

wtsi-npg / genotyping

Components of the WTSI genotype analysis pipeline.
5 stars 7 forks source link

Illuminus workflow doesn't check for required argument plex_manifest #434

Closed keithj closed 7 years ago

keithj commented 7 years ago

If the user forgets this required argument the pipeline will still run for a long time and then fail later:

Attribute (plex_manifest) does not pass the type constraint because: Validation failed for 'Str'
with value undef at accessor WTSI::NPG::Genotyping::QC::Identity::plex_manifest
(defined at /software/gapi/pkg/genotyping/1.13.1/lib/perl5/WTSI/NPG/Genotyping/QC/Identity.pm line 105)
keithj commented 7 years ago

The workflow removes plex_manifest from the arguments to the workflow and then adds it back when calling certain tasks, only if a vcf argument is also supplied. The workflow therefore always fail as there is no VCF to supply.

iainrb commented 7 years ago

The zcall workflow has a similar issue. Fix for illuminus is now passing tests, will implement a similar one for zcall.