A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
GNU Affero General Public License v3.0
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Sample names inherit part of illumina's nomenclature for index and lane #87
We have fastq files which look like COG-ID_S106_L001_R1_001.fastq.gz coming off our illumina hardware, however the pipeline will take the index part S\d+ and lane L\d+ end up appended to the COG-ID in final output, would be nice to remove these so input filename renaming is not required.
We have fastq files which look like
COG-ID_S106_L001_R1_001.fastq.gzcoming off our illumina hardware, however the pipeline will take the index partS\d+and laneL\d+end up appended to the COG-ID in final output, would be nice to remove these so input filename renaming is not required.