Run the alignment/variant-call/consensus logic of the artic pipeline
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
fastq:file
FastQ file containing reads
*.{fastq.gz}
fast5_dir:directory
Directory containing MinION FAST5 files
*
sequencing_summary:file
Path to Guppy sequencing summary
*.{txt}
"primer-schemes/${scheme}/V${scheme_version}/${scheme}.reference.fasta":file
Scheme reference file
"primer-schemes/${scheme}/V${scheme_version}/${scheme}.scheme.bed":file
Scheme BED file
medaka_model_file:file
Medaka model file to use (if option —medaka is set)
*.hdf5
medaka_model_string:string
Medaka model string to use (if option —medaka is set)
scheme:string
Name of the primer scheme
scheme_version:string
Version of the primer scheme
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
