Update DnaCapture dna_capture_var_fastq.py script and related json configs

epam / fonda

Fonda is a framework which offers scalable and automatic analysis of multiple NGS sequencing data types

Apache License 2.0

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Update DnaCapture dna_capture_var_fastq.py script and related json configs #215

Closed syansanofi closed 3 years ago

syansanofi commented 3 years ago

Could we please include the new options in the middleware scripts? I believe they are the following, but please check my list because I am not sure if it is complete.

Databases

BWA_IMG
CONTAMINATION_VCF
ADAPTER_FWD
ADAPTER_REV

all_tools

novoalign_tune

syansanofi commented 3 years ago

Sorry, I was not clear on that part. I think all of them can be specified in the json and not passed in with the exception of novoalign_tune. This parameter should be passed in by middleware. Thank you