modules/dshbio_exportsegments

Export assembly segment sequences in GFA 1.0 format to FASTA format

gfaassemblysegment

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

Description

Export assembly segment sequences in GFA 1.0 format to FASTA format

Input

name:type

description

pattern

`meta{:bash}`
`:map`

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

`gfa{:bash}`
`:file`

Assembly segments in uncompressed or compressed GFA 1.0 format

*.{gfa|gfa.bgz|gfa.gz|gfa.zst}

Output

name:type

description

pattern

`fasta{:bash}`

`meta{:bash}`
`:map`

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

`*.fa.gz{:bash}`
`:file`

Assembly segment sequences in gzipped FASTA format

*.{fa.gz}

`versions{:bash}`

`versions.yml{:bash}`
`:file`

File containing software versions

versions.yml

Tools

dshbio
LGPL-3.0-or-later

Reads, features, variants, assemblies, alignments, genomic range trees, pangenome graphs, and a bunch of random command line tools for bioinformatics. LGPL version 3 or later.

github.com/heuermh/dishevelled-bio

modules/dshbio_exportsegments

Description

Input

`meta{:bash}`
`:map`

`gfa{:bash}`
`:file`

Output

`fasta{:bash}`

`meta{:bash}`
`:map`

`*.fa.gz{:bash}`
`:file`

`versions{:bash}`

`versions.yml{:bash}`
`:file`

Tools

dshbio
LGPL-3.0-or-later

maintainer

get in touch

modules/dshbio_exportsegments

Description

Input

meta{:bash}:map

gfa{:bash}:file

Output

fasta{:bash}

meta{:bash}:map

*.fa.gz{:bash}:file

versions{:bash}

versions.yml{:bash}:file

Tools

dshbio LGPL-3.0-or-later

maintainer

get in touch

`meta{:bash}`
`:map`

`gfa{:bash}`
`:file`

`fasta{:bash}`

`meta{:bash}`
`:map`

`*.fa.gz{:bash}`
`:file`

`versions{:bash}`

`versions.yml{:bash}`
`:file`

dshbio
LGPL-3.0-or-later