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

nf-core/oatk @ 0.0.0-6c4ed3a

An nf-core module for the OATK

organelle mitochondrion plastid PacBio HiFi assembly

Latest version: 0.0.0-6c4ed3a

Total downloads: 12

Source: nf-core/modules

Authors: @ksenia-krasheninnikova

An nf-core module for the OATK

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

include { OATK } from 'nf-core/oatk'

MIT License

Process

`Name`	`OATK`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'Cladonia_norvegica' ]
`reads` file	HiFi reads in FASTA format `*.{fasta,fasta.gz,fa,fa.gz}`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. [ id:'Cladonia_norvegica' ]
`mito_hmm_files` file	HMM profile for mitochondrial gene annotation, with corresponding .h3i, h3f, .h3p, .h3m files from hmmpress `*.{fam,h3i,h3f,h3p,h3m}`

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. [ id:'Cladonia_norvegica' ]
`pltd_hmm_files` file	HMM profile for plastid gene annotation, with corresponding .h3i, h3f, .h3p, .h3m files from hmmpress `*.{fam,h3i,h3f,h3p,h3m}`

Output 12 channels

#1 log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.log` file	log file describing oatk run `*.log`

#2 mito_bed tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*mito.ctg.bed` file	the gene annotation for the MT sequences `*mito.ctg.bed`

#3 mito_gfa tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*mito.gfa` file	the subgraph for the MT genome `*mito.gfa`

#4 pltd_bed tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*pltd.ctg.bed` file	the gene annotation for the PT sequences `*pltd.ctg.bed`

#5 pltd_gfa tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*pltd.gfa` file	the subgraph for the PT genome `*pltd.gfa`

#6 final_gfa tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*utg.final.gfa` file	the GFA file for the final genome assembly `*utg.final.gfa`

#7 mito_fasta tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*mito.ctg.fasta` file	the structure-solved MT contigs `*mito.ctg.fasta`

#8 pltd_fasta tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*pltd.ctg.fasta` file	the structure-solved PT contigs `*pltd.ctg.fasta`

#9 initial_gfa tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*utg.gfa` file	the GFA file for the initial genome assembly `*utg.gfa`

#10 versions_oatk tuple

`${task.process}` string