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