Mercury_Prep_N_Batch: fixes

theiagen / public_health_viral_genomics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, especially SARS-CoV-2

https://public-health-viral-genomics-theiagen.readthedocs.io/

GNU Affero General Public License v3.0

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Mercury_Prep_N_Batch: fixes #206

Closed sage-wright closed 1 year ago

sage-wright commented 1 year ago

make enhancements/fixes to workflow

sage-wright commented 1 year ago

[x] enable different read1/read2 input fastq file name
[ ] speed up gsutil operation by proper usage of the -m flag for multiple files
[x] enable different assembly_fasta name
[ ] enable different assembly_mean_coverage column
[ ] consolidate clearlabs options into single Boolean variable??
- not sure about what ONT uses, will have to investigate