Nextflow Registry | nf-core/snippy/run@0.0.0-6c4ed3a

nf-core/snippy/run @ 0.0.0-6c4ed3a

Rapid haploid variant calling

variant fastq bacteria

Latest version: 0.0.0-6c4ed3a

Total downloads: 10

Source: nf-core/modules

Authors: @rpetit3 @delfiterradas

Maintainers: @rpetit3

Rapid haploid variant calling

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

include { SNIPPY_RUN } from 'nf-core/snippy/run'

MIT License

Process

`Name`	`SNIPPY_RUN`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`reads` file	List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. `*.{fq,fastq,fq.gz,fastq.gz}`

`reference` file	Reference genome in FASTA format `*.{fasta,fna,fa}`

Output 18 channels

#1 bai tuple

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

#2 bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/${prefix}.bam` file	The alignments in BAM format. Includes unmapped, multimapping reads. Excludes duplicates. `*.bam`

#3 bed tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/${prefix}.bed` file	The variants in BED format `*.bed`

#4 csv tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/${prefix}.csv` file	A comma-separated version of the .tab file `*.csv`

#5 gff tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/${prefix}.gff` file	The variants in GFF3 format `*.gff`

#6 log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/${prefix}.log` file	A log file with the commands run and their outputs `*.log`

#7 tab tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/${prefix}.tab` file	A simple tab-separated summary of all the variants `*.tab`

#8 txt tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/${prefix}.txt` file	Tab-separated columnar list of statistics `*.txt`

#9 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/${prefix}.vcf` file	The final annotated variants in VCF format `*.vcf`

#10 html tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/${prefix}.html` file	A HTML version of the .tab file `*.html`

#11 vcf_gz tuple

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