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theiagen / public_health_bioinformatics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.
GNU General Public License v3.0
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[Utilities] Add workflow to rename FASTQ files in a non-destructive manner #266

Closed cimendes closed 10 months ago

cimendes commented 10 months ago

:cool:

:pushpin: Explain the Request

For GISAID compatibility:

To ensure that the FASTQ files are linked correctly, please rename the FASTQ files with the associated EPI_ISL_xxx ID OR Drag & Drop a .txt file containing a list of FASTQ filenames and corresponding FASTA sequence (EPI_ISL_xxx) together with your submission.

To facilitate the process on Terra, a new utility workflow needs to be created implementing the first suggestion on the quote.