Nextflow Registry | nf-core/spades@0.0.0-6c4ed3a

nf-core/spades @ 0.0.0-6c4ed3a

Assembles a small genome (bacterial, fungal, viral)

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @JoseEspinosa @drpatelh @d4straub

Maintainers: @JoseEspinosa @drpatelh @d4straub

Assembles a small genome (bacterial, fungal, viral)

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

include { SPADES } from 'nf-core/spades'

MIT License

Process

`Name`	`SPADES`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`illumina` file	List of input FastQ (Illumina or PacBio CCS reads) files of size 1 and 2 for single-end and paired-end data, respectively. This input data type is required.
`pacbio` file	List of input PacBio CLR FastQ files of size 1.
`nanopore` file	List of input FastQ files of size 1, originating from Oxford Nanopore technology.

`yml` file	Path to yml file containing read information. The raw FASTQ files listed in this YAML file MUST be supplied to the respective illumina/pacbio/nanopore input channel(s) in addition to this YML. File entries in this yml must contain only the file name and no paths. `*.{yml,yaml}`

`hmm` file	File or directory with amino acid HMMs for Spades HMM-guided mode.

Output 8 channels

#1 gfa tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*.fa.gz`
`*.assembly.gfa.gz` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*.gfa.gz`

#2 log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*.fa.gz`
`*.spades.log` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*.spades.log`

#3 contigs tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*.fa.gz`
`*.contigs.fa.gz` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*.fa.gz`

#4 warnings tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*.fa.gz`
`*.warnings.log` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

#5 scaffolds tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*.fa.gz`
`*.scaffolds.fa.gz` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*.fa.gz`

#6 transcripts tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*.fa.gz`
`*.transcripts.fa.gz` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*.fa.gz`

#7 gene_clusters tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*.fa.gz`
`*.gene_clusters.fa.gz` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*.fa.gz`

#8 versions_spades tuple

`${task.process}` string	The process the versions were collected from
`spades` string	The tool name
`spades.py --version 2>&1 \| sed -n 's/^.*SPAdes genome assembler v//p'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage