nf-core_modules/modules/artic/minion/meta.yml

118 lines
3.3 KiB
YAML

name: artic_minion
description: |
Run the alignment/variant-call/consensus logic of the artic pipeline
keywords:
- artic
- aggregate
- demultiplexed reads
tools:
- artic:
description: ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore
homepage: https://artic.readthedocs.io/en/latest/
documentation: https://artic.readthedocs.io/en/latest/
tool_dev_url: https://github.com/artic-network/fieldbioinformatics
doi: ""
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- fastq:
type: file
description: FastQ file containing reads
pattern: "*.{fastq.gz}"
- fast5_dir:
type: directory
description: Directory containing MinION FAST5 files
pattern: "*"
- sequencing_summary:
type: file
description: Path to Guppy sequencing summary
pattern: "*.{txt}"
- primer_scheme_fasta:
type: file
description: |
Sequence of the reference genome used in the scheme in FASTA format
pattern: "*.{reference.fasta}"
- primer_scheme_bed:
type: file
description: |
bed files containing coordinates of each primer in the scheme,
relative to the reference genome
pattern: "*.{scheme.bed}"
- medaka_model_file:
type: file
description: |
Medaka model file to use (if option --medaka is set)
pattern: "*.hdf5"
- medaka_model_string:
type: value
description: |
Medaka model string to use (if option --medaka is set)
pattern: "*"
- scheme:
type: value
description: Name of the primer scheme
- scheme_version:
type: value
description: Version of the primer scheme
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- results:
type:
description: Aggregated FastQ files
pattern: "*.fastq.gz"
- bam:
type: file
description: BAM file
pattern: "*.{sorted.bam}"
- bai:
type: file
description: BAM index file
pattern: "*.{sorted.bai}"
- bam_trimmed:
type: file
description: BAM file with the primers left on
pattern: "*.{trimmed.rg.sorted.bam}"
- bai_trimmed:
type: file
description: BAM index file of bam_trimmed
pattern: "*.{sorted.bai}"
- bam_primertrimmed:
type: file
description: BAM containing reads after primer-binding site trimming
pattern: "*.{trimmed.rg.sorted.bam}"
- bai_primertrimmed:
type: file
description: BAM index file of bam_primertrimmed
pattern: "*.{primertrimmed.rg.sorted.bam.bai}"
- fasta:
type: file
description: FAST file with consensus sequence
pattern: "*.{consensus.fasta}"
- vcf:
type: file
description: VCF file containing detected variants passing quality filter
pattern: "*.{pass.vcf.gz}"
- tbi:
type: file
description: VCF index
pattern: "*.{pass.vcf.gz.tbi}"
- json:
type: file
description: JSON file for MultiQC
pattern: "*.json"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@joseespinosa"
- "@drpatelh"