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

nf-core/canu @ 0.0.0-6c4ed3a

Accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads.

Assembly pacbio hifi nanopore

Latest version: 0.0.0-6c4ed3a

Total downloads: 15

Source: nf-core/modules

Authors: @scorreard

Maintainers: @scorreard

Accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads.

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

include { CANU } from 'nf-core/canu'

MIT License

Process

`Name`	`CANU`

Input 3 channels

#1 tuple

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

`mode` string	Canu mode depending on the input data (source and error rate) `-pacbio\|-nanopore\|-pacbio-hifi`

`genomesize` string	An estimate of the size of the genome. Common suffices are allowed, for example, 3.7m or 2.8g `<number>[g\|m\|k]`

Output 11 channels

#1 report tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.report` file	Most of the analysis reported during assembly `*.report`

#2 contigs tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.unassembled.fasta.gz` file	Reads and low-coverage contigs which could not be incorporated into the primary assembly. `*.unassembled.fasta`

#3 assembly tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.contigs.fasta.gz` file	Everything which could be assembled and is the full assembly, including both unique, repetitive, and bubble elements. `*.contigs.fasta`

#4 metadata tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.contigs.layout` file	(undocumented) `*.contigs.layout`

#5 contig_info tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.contigs.layout.tigInfo` file	A list of the contigs, lengths, coverage, number of reads and other metadata. Essentially the same information provided in the FASTA header line. `*.contigs.layout.tigInfo`

#6 versions_canu tuple

`${task.process}` string	The name of the process
`canu` string	The name of the tool
`2.3` string	The expression to obtain the version of the tool

#7 contig_position tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.contigs.layout.readToTig` file	The position of each read in a contig `*.contigs.layout.readToTig`

#8 corrected_reads tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.correctedReads.fasta.gz` file	The reads after correction. `*.correctedReads.fasta.gz`

#9 versions_minimap2 tuple

`${task.process}` string	The name of the process
`minimap2` string	The name of the tool
`minimap2 --version` eval	The expression to obtain the version of the tool

#10 versions_samtools tuple

`${task.process}` string	The name of the process