modules/plasmidid

assembles bacterial plasmids

assemblyplasmidbacterial

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

Description

assembles bacterial plasmids

Input

name:type

description

pattern

`meta`
`:map`

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

`scaffold`
`:file`

Fasta file containing scaffold

`fasta`
`:file`

FASTA reference file

*.{fasta,fa}

Output

name:type

description

pattern

`html`

`meta`
`:map`

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

`${prefix}/*final_results.html`
`:file`

html file with results rendered

*.{html}

`tab`

`meta`
`:map`

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

`${prefix}/*final_results.tab`
`:file`

Results in a tabular file

*.{tab}

`images`

`meta`
`:map`

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

`${prefix}/images/`
`:directory`

Directory containing the images produced by plasmidid

images

`logs`

`meta`
`:map`

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

`${prefix}/logs/`
`:directory`

Directory containing the logs produced by plasmidid

logs

`data`

`meta`
`:map`

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

`${prefix}/data/`
`:directory`

Directory containing the data produced by plasmidid

data

`database`

`meta`
`:map`

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

`${prefix}/database/`
`:directory`

Directory containing the database produced by plasmidid

database

`fasta_files`

`meta`
`:map`

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

`${prefix}/fasta_files/`
`:directory`

Directory containing the fasta files produced by plasmidid

fasta_files

`kmer`

`meta`
`:map`

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

`${prefix}/kmer/`
`:directory`

Directory containing the kmer files produced by plasmidid

database

`versions_plasmidid`

`${task.process}`
`:string`

The name of the process

`plasmidid`
`:string`

The name of the tool

`plasmidID --version 2>&1 | sed 's/^plasmidID //'`
`:eval`

The expression to obtain the version of the tool

`versions_parallel`

`${task.process}`
`:string`

The name of the process

`parallel`
`:string`

The name of the tool

`parallel --version | sed '1!d;s/GNU parallel //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`plasmidid`
`:string`

The name of the tool

`plasmidID --version 2>&1 | sed 's/^plasmidID //'`
`:eval`

The expression to obtain the version of the tool

`${task.process}`
`:string`

The name of the process

`parallel`
`:string`

The name of the tool

`parallel --version | sed '1!d;s/GNU parallel //'`
`:eval`

The expression to obtain the version of the tool

Tools

plasmidid
GPL v3

Pipeline for plasmid identification and reconstruction

github.com/BU-ISCIII/plasmidID/wiki github.com/BU-ISCIII/plasmidID#readme https://github.com/BU-ISCIII/plasmidID

modules/plasmidid

Description

Input

meta :map

scaffold :file

fasta :file

Output

html

meta :map

${prefix}/*final_results.html :file

tab

meta :map

${prefix}/*final_results.tab :file

images

meta :map

${prefix}/images/ :directory

logs

meta :map

${prefix}/logs/ :directory

data

meta :map

${prefix}/data/ :directory

database

meta :map

${prefix}/database/ :directory

fasta_files

meta :map

${prefix}/fasta_files/ :directory

kmer

meta :map

${prefix}/kmer/ :directory

versions_plasmidid

${task.process} :string

plasmidid :string

plasmidID --version 2>&1 | sed 's/^plasmidID //' :eval

versions_parallel

${task.process} :string

parallel :string

parallel --version | sed '1!d;s/GNU parallel //' :eval

Topics

versions

${task.process} :string

plasmidid :string

plasmidID --version 2>&1 | sed 's/^plasmidID //' :eval

${task.process} :string

parallel :string

parallel --version | sed '1!d;s/GNU parallel //' :eval

Tools

plasmididGPL v3

included in

maintainers

get in touch

`meta`
`:map`

`scaffold`
`:file`

`fasta`
`:file`

`html`

`meta`
`:map`

`${prefix}/*final_results.html`
`:file`

`tab`

`meta`
`:map`

`${prefix}/*final_results.tab`
`:file`

`images`

`meta`
`:map`

`${prefix}/images/`
`:directory`

`logs`

`meta`
`:map`

`${prefix}/logs/`
`:directory`

`data`

`meta`
`:map`

`${prefix}/data/`
`:directory`

`database`

`meta`
`:map`

`${prefix}/database/`
`:directory`

`fasta_files`

`meta`
`:map`

`${prefix}/fasta_files/`
`:directory`

`kmer`

`meta`
`:map`

`${prefix}/kmer/`
`:directory`

`versions_plasmidid`

`${task.process}`
`:string`

`plasmidid`
`:string`

`plasmidID --version 2>&1 | sed 's/^plasmidID //'`
`:eval`

`versions_parallel`

`${task.process}`
`:string`

`parallel`
`:string`

`parallel --version | sed '1!d;s/GNU parallel //'`
`:eval`

`versions`

`${task.process}`
`:string`

`plasmidid`
`:string`

`plasmidID --version 2>&1 | sed 's/^plasmidID //'`
`:eval`

`${task.process}`
`:string`

`parallel`
`:string`

`parallel --version | sed '1!d;s/GNU parallel //'`
`:eval`

plasmidid
GPL v3