Run the alignment/variant-call/consensus logic of the artic pipeline
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
fastq{:bash}
:file
FastQ file containing reads
*.{fastq.gz}
meta2{:bash}
Groovy Map containing model information e.g. [ id:‘test’, single_end:false ]
model_dir{:bash}
:directory
Path containing clair3 models, defaults to models packaged with conda installation
*
model{:bash}
: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{:bash}
Groovy Map containing scheme information e.g. [ id:‘test’, single_end:false ]
fasta{:bash}
Scheme reference fasta file
*.{fasta}
bed{:bash}
Scheme BED file
*.{bed}
results{:bash}
${prefix}.*{:bash}
Aggregated FastQ files
*.fastq.gz
bam{:bash}
${prefix}.sorted.bam{:bash}
BAM file
*.{sorted.bam}
bai{:bash}
${prefix}.sorted.bam.bai{:bash}
BAM index file
*.{sorted.bai}
bam_trimmed{:bash}
${prefix}.trimmed.rg.sorted.bam{:bash}
BAM file with the primers left on
*.{trimmed.rg.sorted.bam}
bai_trimmed{:bash}
${prefix}.trimmed.rg.sorted.bam.bai{:bash}
BAM index file of bam_trimmed
bam_primertrimmed{:bash}
${prefix}.primertrimmed.rg.sorted.bam{:bash}
BAM containing reads after primer-binding site trimming
bai_primertrimmed{:bash}
${prefix}.primertrimmed.rg.sorted.bam.bai{:bash}
BAM index file of bam_primertrimmed
*.{primertrimmed.rg.sorted.bam.bai}
${prefix}.consensus.fasta{:bash}
FAST file with consensus sequence
*.{consensus.fasta}
vcf{:bash}
${prefix}.pass.vcf.gz{:bash}
VCF file containing detected variants passing quality filter
*.{pass.vcf.gz}
tbi{:bash}
${prefix}.pass.vcf.gz.tbi{:bash}
VCF index
*.{pass.vcf.gz.tbi}
json{:bash}
*.json{:bash}
JSON file for MultiQC
*.json
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore
