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wtsi-team112 / ncov2019-artic-nf

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019 - adapted to run at the Wellcome Sanger Institute
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Issue3 cramtofastq #7

Closed JonKeatley112 closed 4 years ago

JonKeatley112 commented 4 years ago

Added --cram option to switch input from a directory of fastq to a directory for cram.

Currently only applies to the --illumina branch

Example usage:

bash ~/nextflow run ./ncov2019-artic-nf -profile lsf,singularity --illumina --directory ./cram/ --cram