Please see the Viridian Workflow Wiki for full documentation.
The recommended method is to use a pre-built Docker or Singularity container (see the wiki for how to build your own).
Both the Docker and Singularity container have the main script
viridian_workflow installed.
Get a Docker image of the latest release:
docker pull ghcr.io/iqbal-lab-org/cte:latest
All Docker images are listed in the packages page.
Releases
include a Singularity image to download.
Each release has a singularity image file called
viridian_workflow_vX.Y.Z.img, where X.Y.Z is the release version.
To run on paired Illumina reads:
viridian_workflow run_one_sample \
--tech illumina
--ref_fasta data/MN908947.fasta \
--reads1 reads_1.fastq.gz \
--reads2 reads_2.fastq.gz \
--outdir OUT
To run on unpaired nanopore reads:
viridian_workflow run_one_sample \
--tech ont
--ref_fasta data/MN908947.fasta \
--reads reads.fastq.gz \
--outdir OUT
The FASTA file in those commands can be found in the viridian_workflow/amplicon_scheme_data/
directory of this repository.
Other options:
--sample_name MY_NAME: use this to change the sample name (default is "sample") that is put in the final FASTA file, BAM file, and VCF file.--keep_bam: use this option to keep the BAM file of original input reads mapped to the reference genome.--force: use with caution - it will overwrite the output directory if it already exists.
The default files in the output directory are:
consensus.fa: a FASTA file of the consensus sequence.variants.vcf: a VCF file of the identified variants between the consensus sequence and the reference genome.log.json: contains logging information for the viridian workflow run.
If the option --keep_bam is used, then a sorted BAM file of the reads mapped
to the reference will also be present, called
reference_mapped.bam (and its index file reference_mapped.bam.bai).