Description

Run the alignment/variant-call/consensus logic of the artic pipeline

Input

Name (Type)
Description
Pattern

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_scheme_fasta (file)

Sequence of the reference genome used in the scheme in FASTA format

*.{reference.fasta}

primer_scheme_bed (file)

bed files containing coordinates of each primer in the scheme,
relative to the reference genome

*.{scheme.bed}

medaka_model_file (file)

Medaka model file to use (if option —medaka is set)

*.hdf5

medaka_model_string (value)

Medaka model string to use (if option —medaka is set)

*

scheme (value)

Name of the primer scheme

scheme_version (value)

Version of the primer scheme

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

results (file)

Aggregated FastQ files

*.fastq.gz

bam (file)

BAM file

*.{sorted.bam}

bai (file)

BAM index file

*.{sorted.bai}

bam_trimmed (file)

BAM file with the primers left on

*.{trimmed.rg.sorted.bam}

bai_trimmed (file)

BAM index file of bam_trimmed

*.{sorted.bai}

bam_primertrimmed (file)

BAM containing reads after primer-binding site trimming

*.{trimmed.rg.sorted.bam}

bai_primertrimmed (file)

BAM index file of bam_primertrimmed

*.{primertrimmed.rg.sorted.bam.bai}

fasta (file)

FAST file with consensus sequence

*.{consensus.fasta}

vcf (file)

VCF file containing detected variants passing quality filter

*.{pass.vcf.gz}

tbi (file)

VCF index

*.{pass.vcf.gz.tbi}

json (file)

JSON file for MultiQC

*.json

versions (file)

File containing software versions

versions.yml
included in
viralrecon
maintainers
Github user joseespinosa
Github user drpatelh
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Tools

artic
MIT

ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore

artic.readthedocs.io/en/latest https://github.com/artic-network/fieldbioinformatics