Run the alignment/variant-call/consensus logic of the artic pipeline
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
fastq
:file
FastQ file containing reads
*.{fastq.gz}
meta2
Groovy Map containing model information e.g. [ id:‘test’, single_end:false ]
model_dir
:directory
Path containing clair3 models, defaults to models packaged with conda installation
*
model
:string
The model to use for clair3, if not provided the pipeline will try to figure it out the appropriate model from the read fastq
meta3
Groovy Map containing scheme information e.g. [ id:‘test’, single_end:false ]
fasta
Scheme reference fasta file
*.{fasta}
bed
Scheme BED file
*.{bed}
results
${prefix}.*
Aggregated FastQ files
*.fastq.gz
bam
${prefix}.sorted.bam
BAM file
*.{sorted.bam}
bai
${prefix}.sorted.bam.bai
BAM index file
*.{sorted.bai}
bam_trimmed
${prefix}.trimmed.rg.sorted.bam
BAM file with the primers left on
*.{trimmed.rg.sorted.bam}
bai_trimmed
${prefix}.trimmed.rg.sorted.bam.bai
BAM index file of bam_trimmed
bam_primertrimmed
${prefix}.primertrimmed.rg.sorted.bam
BAM containing reads after primer-binding site trimming
bai_primertrimmed
${prefix}.primertrimmed.rg.sorted.bam.bai
BAM index file of bam_primertrimmed
*.{primertrimmed.rg.sorted.bam.bai}
${prefix}.consensus.fasta
FAST file with consensus sequence
*.{consensus.fasta}
vcf
${prefix}.pass.vcf.gz
VCF file containing detected variants passing quality filter
*.{pass.vcf.gz}
tbi
${prefix}.pass.vcf.gz.tbi
VCF index
*.{pass.vcf.gz.tbi}
json
*.json
JSON file for MultiQC
versions
versions.yml
File containing software versions
ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore
