mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-27 15:53:16 -05:00
113 lines
3.2 KiB
YAML
113 lines
3.2 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:
|
|
type: file
|
|
description: |
|
|
Medaka model 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"
|
|
- version:
|
|
type: file
|
|
description: File containing software version
|
|
pattern: "*.{version.txt}"
|
|
|
|
authors:
|
|
- "@joseespinosa"
|
|
- "@drpatelh"
|