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:map
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:map
Groovy Map containing scheme information e.g. [ id:‘test’, single_end:false ]
fasta:file
Scheme reference fasta file
*.{fasta}
bed:file
Scheme BED file
*.{bed}
results
${prefix}.*:file
Aggregated FastQ files
*.fastq.gz
bam
${prefix}.sorted.bam:file
BAM file
*.{sorted.bam}
bai
${prefix}.sorted.bam.bai:file
BAM index file
*.{sorted.bai}
bam_trimmed
${prefix}.trimmed.rg.sorted.bam:file
BAM file with the primers left on
*.{trimmed.rg.sorted.bam}
bai_trimmed
${prefix}.trimmed.rg.sorted.bam.bai:file
BAM index file of bam_trimmed
bam_primertrimmed
${prefix}.primertrimmed.rg.sorted.bam:file
BAM containing reads after primer-binding site trimming
bai_primertrimmed
${prefix}.primertrimmed.rg.sorted.bam.bai:file
BAM index file of bam_primertrimmed
*.{primertrimmed.rg.sorted.bam.bai}
fasta
${prefix}.consensus.fasta:file
FAST file with consensus sequence
*.{consensus.fasta}
vcf
${prefix}.pass.vcf.gz:file
VCF file containing detected variants passing quality filter
*.{pass.vcf.gz}
tbi
${prefix}.pass.vcf.gz.tbi:file
VCF index
*.{pass.vcf.gz.tbi}
json
*.json:file
JSON file for MultiQC
*.json
versions
versions.yml:file
File containing software versions
versions.yml
ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore
