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

nf-core/merquryfk/merquryfk @ 0.0.0-6c4ed3a

FastK based version of Merqury

Merqury reference-free assembly evaluation

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @mahesh-panchal @yumisims

Maintainers: @mahesh-panchal @yumisims

FastK based version of Merqury

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

include { MERQURYFK_MERQURYFK } from 'nf-core/merquryfk/merquryfk'

MIT License

Process

`Name`	`MERQURYFK_MERQURYFK`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fastk_hist` file	A histogram files from the program FastK `*.hist`
`fastk_ktab` file	Histogram ktab files from the program FastK (option -t) `.ktab`
`assembly` file	Genome (primary) assembly files (fasta format) `.fasta`
`haplotigs` file	Assembly haplotigs (fasta format) `.fasta`

#2 tuple

`meta2` map	Groovy Map containing maternal sample information e.g. [ id:'test', single_end:false ]
`mathaptab` file	trio maternal histogram ktab files from the program FastK (option -t) `.ktab`

#3 tuple

`meta3` map	Groovy Map containing paternal sample information e.g. [ id:'test', single_end:false ]
`pathaptab` file	trio paternal histogram ktab files from the program FastK (option -t) `.ktab`

Output 10 channels

#1 qv tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.qv` file	error and qv of each assembly as a whole `*.qv`

#2 bed tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.*_only.bed` file	Assembly only kmer positions not supported by reads in bed format `*_only.bed`

#3 stats tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.completeness.stats` file	Assembly statistics file `*.completeness.stats`

#4 images tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.{pdf,png}` file	Output graphs from MerquryFK `*.{pdf,png}`

#5 versions_r tuple

`${task.process}` string	Name of the process
`R` string	Name of the tool
`R --version \| sed "1!d; s/.version //; s/ .//"` eval	The expression to obtain the version of the tool

#6 assembly_qv tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.*.qv` file	error and qv table for each scaffold of the assembly `*.qv`

#7 versions_fastk tuple

`${task.process}` string	Name of the process
`fastk` string	Name of the tool
`1.2` string	The expression to obtain the version of the tool

#8 phased_block_bed tuple

`meta` map