type/

contiguate draft genome assembly

genomeassemblycontiguate

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

Description

contiguate draft genome assembly

Input

name:type

description

pattern

`meta:map`

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

]

`scaffold:file`

Fasta file containing scaffold

*.{fasta,fa}

`fasta:file`

FASTA reference file

*.{fasta,fa}

Output

name:type

description

pattern

`results`

`meta:map`

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

]

`.abacas:file`

List containing abacas output files [ ‘test.abacas.bin’, ‘test.abacas.fasta’, ‘test.abacas.gaps’, ‘test.abacas.gaps.tab’, ‘test.abacas.nucmer.delta’, ‘test.abacas.nucmer.filtered.delta’, ‘test.abacas.nucmer.tiling’, ‘test.abacas.tab’, ‘test.abacas.unused.contigs.out’, ‘test.abacas.MULTIFASTA.fa’ ]

*.{abacas}*

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

abacas
GPL v2-or-later

ABACAS is intended to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence.

http://abacas.sourceforge.net/documentation 10.1093/bioinformatics/btp347

type/

Description

Input

`meta:map`

`scaffold:file`

`fasta:file`

Output

`results`

`meta:map`

`.abacas:file`

`versions`

`versions.yml:file`

Tools

abacas
GPL v2-or-later

included in

maintainers

get in touch

type/

Description

Input

meta:map

scaffold:file

fasta:file

Output

results

meta:map

*.abacas*:file

versions

versions.yml:file

Tools

abacas GPL v2-or-later

included in

maintainers

get in touch

`meta:map`

`scaffold:file`

`fasta:file`

`results`

`meta:map`

`.abacas:file`

`versions`

`versions.yml:file`

abacas
GPL v2-or-later