modules/oatk

An nf-core module for the OATK

organellemitochondrionplastidPacBioHiFiassembly

https://github.com/nf-core/modules/[...]/modules/nf-core/oatk

Description

An nf-core module for the OATK

Input

name:type

description

pattern

`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}

`mito_hmm`
`:file`

mitochondria gene annotation HMM profile database

*.{fa,fam}

`mito_hmm_h3f`
`:file`

mitochondria gene annotation HMM profile binary auxfile

*.{h3f}

`mito_hmm_h3i`
`:file`

mitochondria gene annotation HMM profile binary auxfile

*.{h3i}

`mito_hmm_h3m`
`:file`

mitochondria gene annotation HMM profile binary auxfile

*.{h3m}

`mito_hmm_h3p`
`:file`

mitochondria gene annotation HMM profile binary auxfile

*.{h3p}

`pltd_hmm`
`:file`

plastid gene annotation HMM profile database

*.{fa,fam}

`pltd_hmm_h3f`
`:file`

plastid gene annotation HMM profile binary auxfile

*.{h3f}

`pltd_hmm_h3i`
`:file`

plastid gene annotation HMM profile binary auxfile

*.{h3i}

`pltd_hmm_h3m`
`:file`

plastid gene annotation HMM profile binary auxfile

*.{h3m}

`pltd_hmm_h3p`
`:file`

plastid gene annotation HMM profile binary auxfile

*.{h3p}

Output

name:type

description

pattern

`mito_fasta`

`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

`pltd_fasta`

`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

`mito_bed`

`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

`pltd_bed`

`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

`mito_gfa`

`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

`pltd_gfa`

`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

`annot_mito_txt`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*annot_mito.txt`
`:file`

the MT gene annotation file over all assembled sequences

*annot_mito.txt

`annot_pltd_txt`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*annot_pltd.txt`
`:file`

the PT gene annotation file over all assembled sequences

*annot_pltd.txt

`clean_gfa`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*utg.clean.gfa`
`:file`

the GFA file for the clean genome assembly

*utg.clean.gfa

`final_gfa`

`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

`initial_gfa`

`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

`multiplex_gfa`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*utg.multiplex.gfa`
`:file`

the mutliplexed GFA file

*utg.multiplex.gfa

`unzip_gfa`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*utg.unzip.gfa`
`:file`

the unzipped GFA file

*utg.unzip.gfa

`versions`

`versions.yml`
`:file`

File containing software versions

versions.yml

Tools

oatk
MIT

An organelle genome assembly toolkit

github.com/c-zhou/oatk 10.5281/zenodo.10400173