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magicDGS / ReadTools

A Universal Toolkit for Handling Sequence Data from Different Sequencing Platforms
https://magicdgs.github.io/ReadTools/
MIT License
6 stars 3 forks source link

Figure out why barclay warnings pop-up with the trimming arguments #350

Closed magicDGS closed 6 years ago

magicDGS commented 6 years ago

After #347, the trimming arguments produce the following warnings for the readtoolsDoc task:

15:30:45.743 WARN  DefaultDocWorkUnitHandler - Could not access the field definition for backtrace while searching for userTrimmerNames, presumably because the field is inaccessible
15:30:45.743 WARN  DefaultDocWorkUnitHandler - Could not access the field definition for backtrace while searching for userTrimmerNames, presumably because the field is inaccessible
15:30:45.743 WARN  DefaultDocWorkUnitHandler - Could not access the field definition for backtrace while searching for userTrimmerNames, presumably because the field is inaccessible
15:30:46.004 WARN  DefaultDocWorkUnitHandler - Could not access the field definition for backtrace while searching for userTrimmerNames, presumably because the field is inaccessible
15:30:46.004 WARN  DefaultDocWorkUnitHandler - Could not access the field definition for backtrace while searching for userTrimmerNames, presumably because the field is inaccessible
15:30:46.004 WARN  DefaultDocWorkUnitHandler - Could not access the field definition for backtrace while searching for userTrimmerNames, presumably because the field is inaccessible
15:30:46.026 WARN  DefaultDocWorkUnitHandler - Could not access the field definition for backtrace while searching for disabledTrimmers, presumably because the field is inaccessible
15:30:46.026 WARN  DefaultDocWorkUnitHandler - Could not access the field definition for backtrace while searching for disabledTrimmers, presumably because the field is inaccessible
15:30:46.027 WARN  DefaultDocWorkUnitHandler - Could not access the field definition for backtrace while searching for disabledTrimmers, presumably because the field is inaccessible
15:30:46.053 WARN  DefaultDocWorkUnitHandler - Could not access the field definition for backtrace while searching for disableAllDefaultTrimmers, presumably because the field is inaccessible
15:30:46.053 WARN  DefaultDocWorkUnitHandler - Could not access the field definition for backtrace while searching for disableAllDefaultTrimmers, presumably because the field is inaccessible
15:30:46.053 WARN  DefaultDocWorkUnitHandler - Could not access the field definition for backtrace while searching for disableAllDefaultTrimmers, presumably because the field is inaccessible

Nevertheless, arguments are correctly populated into the markdown and json. Thus, this looks like a wierd behaviour of barclay...

magicDGS commented 6 years ago

Maybe this might be solved by the Barclay update in GATK4 (barclay 2.0.0)