Cromwell GATK json list of files

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Kristian Unger

• April 16, 2020 07:41

I want to use GATK workflows such as seq-format-conversion on slurm. In order to apply the workflow on a pair of fastqs several parameters need to be defined in a json per file-pair. In the moment I am writing a rather clumsy R script doing that job and I wonder if there is a more elegant way scripting the generation of jsons for a batch of input files.

a) GATK version used

Docker broadinstitute/gatk:latest

b) Exact GATK commands used

paired-fastq-to-unmapped-bam.inputs.json

c) The entire error log if applicable.

NA

 

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  Bhanu Gandham

  • April 16, 2020 13:43

  Hi Kristian Unger

   

  This is a question for the WDL team. I will have someone from the WDL team get back to you.

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  Kristian Unger

  • April 16, 2020 19:22

  Super! Thank you! Look forward getting in touch with your collegue!

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  Jason Cerrato

  • April 17, 2020 18:39

  Hi Kristian Unger,

  I see that you're looking for scripting advice, rather than WDL advice. In this case, I recommend writing a post on http://bioinformatics.stackexchange.com/ with the tag 'Cromwell'. This way you can get advice straight from our Cromwell engineers, who will likely be more helpful.

  It will be helpful to link to the current script you are working and detail what kinds of improvements you are looking for. I hope you find a more elegant solution!

  If you have any questions about GATK or WDL, please don't hesitate to let us know!

  Kind regards,

  Jason

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