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GEMmaker uses the script implicit variable baseDir in several of its example scripts. As of 20.04.0 Nextflow has deprecated baseDir and instead prefers user to use projectDir and launchDir. https://www.nextflow.io/docs/latest/script.html
We already use the projectDir nomenclature when reporting directories at the beginning of GEMmaker. baseDir references should be changed everywhere within GEMmaker.
Description of the bug
GEMmaker uses the script implicit variable
baseDir
in several of its example scripts. As of 20.04.0 Nextflow has deprecated baseDir and instead prefers user to useprojectDir
andlaunchDir
. https://www.nextflow.io/docs/latest/script.htmlWe already use the
projectDir
nomenclature when reporting directories at the beginning of GEMmaker.baseDir
references should be changed everywhere within GEMmaker.Command used and terminal output
No response
Relevant files
No response
System information
No response
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