Nextflow Registry | nf-core/ragtag/patch@0.0.0-6c4ed3a

nf-core/ragtag/patch @ 0.0.0-6c4ed3a

Homology-based assembly patching: Make continuous joins and fill gaps in 'target.fa' using sequences from 'query.fa'

assembly consensus ragtag patch

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @nschan

Maintainers: @nschan

Homology-based assembly patching: Make continuous joins and fill gaps in 'target.fa' using sequences from 'query.fa'

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

include { RAGTAG_PATCH } from 'nf-core/ragtag/patch'

MIT License

Process

`Name`	`RAGTAG_PATCH`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`target` file	Target assembly `*.{fasta,fasta.gz}`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. [ id:'test' ]
`query` file	Query assembly `*.{fasta,fasta.gz}`

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. [ id:'test' ]
`exclude` file	list of target sequences to ignore `*.txt`

#4 tuple

`meta4` map	Groovy Map containing sample information e.g. [ id:'test' ]
`skip` file	list of query sequences to ignore `*.txt`

Output 10 channels

#1 stderr tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.patch.err` file	Standard error logging for all external RagTag commands `*.patch.err`

#2 patch_agp tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.patch.agp` file	AGP file defining how ragtag.patch.fasta is built `*.patch.agp`

#3 patch_fasta tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.patch.fasta` file	FASTA file containing the patched assembly `*.patch.fasta`

#4 qry_rename_agp tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.rename.agp` file	An AGP file defining the new names for query sequences `*.rename.agp`

#5 versions_ragtag tuple

`${task.process}` string	The name of the process
`ragtag` string	The name of the tool
`ragtag.py -v \| sed 's/v//'` eval	The expression to obtain the version of the tool

#6 qry_rename_fasta tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.rename.fasta` file	A FASTA file with the original query sequence, but with new names `*.rename.fasta`

#7 target_splits_agp tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.ctg.agp` file	An AGP file defining how the target assembly was split at gaps `*.ctg.agp`

#8 assembly_alignments tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`.ragtag.patch.asm.` file	Assembly alignment files `.ragtag.patch.asm.`

#9 target_splits_fasta tuple