merrimanlab / nesi_gatk Goto Github PK
View Code? Open in Web Editor NEWworkflow for GATK on NeSI
License: MIT License
workflow for GATK on NeSI
License: MIT License
Be able to use the nesi project code specified on invocation of the job controller to then be used for all slurm jobs
include extra statuses from the globus transfer status query to interpreted in the jobs process script eg timeout so that a restart transfer can be done
main extra status is 'FAILED"
upon failing due to too many failed ssh attempts the sample id is not added to the failed list. It is not outputted as a completed sample either
Use optional --sample= argument to specify a single sample to be run from the sample file
implement compression of the g.vcf to reduce total download size
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