Nextflow Registry | nf-core/artic/minion@0.0.0-6c4ed3a

nf-core/artic/minion @ 0.0.0-6c4ed3a

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

artic aggregate demultiplexed reads

Latest version: 0.0.0-6c4ed3a

Total downloads: 4

Source: nf-core/modules

Authors: @joseespinosa @drpatelh

Maintainers: @joseespinosa @drpatelh

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

Add the following snippet to your workflow script to include this module.

include { ARTIC_MINION } from 'nf-core/artic/minion'

MIT License

Process

`Name`	`ARTIC_MINION`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fastq` file	FastQ file containing reads `*.{fastq.gz}`

#2 tuple

`meta2` map	Groovy Map containing model information e.g. [ id:'test', single_end:false ]
`model_dir` directory	Path containing clair3 models, defaults to models packaged with conda installation `*`
`model` string	The model to use for clair3, if not provided the pipeline will try to figure it out the appropriate model from the read fastq

#3 tuple

`meta3` map	Groovy Map containing scheme information e.g. [ id:'test', single_end:false ]
`fasta` file	Scheme reference fasta file `*.{fasta}`
`bed` file	Scheme BED file `*.{bed}`

`hdf5_plugin_path` directory	Optional path to HDF5 plugin library

Output 12 channels

#1 bai tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.sorted.bam.bai` file	BAM index file `*.{sorted.bai}`

#2 bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.sorted.bam` file	BAM file `*.{sorted.bam}`

#3 tbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.pass.vcf.gz.tbi` file	VCF index `*.{pass.vcf.gz.tbi}`

#4 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.pass.vcf.gz` file	VCF file containing detected variants passing quality filter `*.{pass.vcf.gz}`

#5 json tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.json` file	JSON file for MultiQC `*.json`

#6 fasta tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.consensus.fasta` file	FAST file with consensus sequence `*.{consensus.fasta}`

#7 results tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.*` file	Aggregated FastQ files `*.fastq.gz`

#8 bai_trimmed tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.trimmed.rg.sorted.bam.bai` file	BAM index file of bam_trimmed `*.{sorted.bai}`