Samples not processed via DNAnexus have no job-id and fails

eastgenomics / eggd_generate_variant_workbook

DNAnexus app for generating xlsx variant workbooks

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Samples not processed via DNAnexus have no job-id and fails #33

Closed jethror1 closed 4 years ago

jethror1 commented 4 years ago

Tried running vcf2xls with vcfs that were generated outside of DNAnexus & therefore have no job-id attached to them, causes the following to happen and the app fails:

++ dx describe --delim _ Sample16.refseq_nirvana203.annotated.vcf ++ grep job- ++ cut -d -f2

job_id=

Needs a default job id or similar setting to allow it to continue.

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Yu-jinKim commented 4 years ago

Either we can have another option to specify whether it's a dnanexus vcf or check if the dx describe returns anything and continue without the job id. Need Matt's input on that I think

jethror1 commented 4 years ago

Fixed by checking the returned dx describe for job id, if not present sets id's to "Unknown" which is then in the output file.

Changes in fix_id_bug branch.