modules/getorganelle_fromreads

Assembles organelle genomes from genomic data

assemblyorganellemitochondriaillumina

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

Description

Assembles organelle genomes from genomic data

Input

name:type

description

pattern

`meta`
`:map`

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

`fastq`
`:file`

Input fastq files

*.{fastq.gz}

`organelle_type`
`:string`

Type of database, esp. embplant_pt (embryophyta plant plastome), other_pt (non-embryophyta plant plastome), embplant_mt (plant mitochondrion), embplant_nr (plant nuclear ribosomal RNA), animal_mt (animal mitochondrion), and fungus_mt (fungus mitochondrion), fungus_nr (fungus nuclear ribosomal RNA)

`db`
`:directory`

GetOrganelle database

Output

name:type

description

pattern

`fasta`

`meta`
`:map`

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

`results/${prefix}.${organelle_type}.fasta.gz`
`:file`

Complete or partial organelle sequences

*.fasta.gz

`etc`

`results/*`
`:file`

Other output files

`versions_getorganelle`

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

The name of the process

`getorganelle_from_reads`
`:string`

The name of the tool

`get_organelle_from_reads.py --version 2>&1 | sed -n 's/GetOrganelle //p'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`getorganelle_from_reads`
`:string`

The name of the tool

`get_organelle_from_reads.py --version 2>&1 | sed -n 's/GetOrganelle //p'`
`:eval`

The expression to obtain the version of the tool

Tools

getorganelle
GPL v3

Get organelle genomes from genome skimming data

github.com/Kinggerm/GetOrganelle 10.1186/s13059-020-02154-5

modules/getorganelle_fromreads

Description

Input

`meta`
`:map`

`fastq`
`:file`

`organelle_type`
`:string`

`db`
`:directory`

Output

`fasta`

`meta`
`:map`

`results/${prefix}.${organelle_type}.fasta.gz`
`:file`

`etc`

`results/*`
`:file`

`versions_getorganelle`

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

`getorganelle_from_reads`
`:string`

`get_organelle_from_reads.py --version 2>&1 | sed -n 's/GetOrganelle //p'`
`:eval`

Topics

`versions`

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

`getorganelle_from_reads`
`:string`

`get_organelle_from_reads.py --version 2>&1 | sed -n 's/GetOrganelle //p'`
`:eval`

Tools

getorganelle
GPL v3

maintainer

get in touch

modules/getorganelle_fromreads

Description

Input

meta:map

fastq:file

organelle_type:string

db:directory

Output

fasta

meta:map

results/${prefix}.${organelle_type}.fasta.gz:file

etc

results/*:file

versions_getorganelle

${task.process}:string

getorganelle_from_reads:string

get_organelle_from_reads.py --version 2>&1 | sed -n 's/GetOrganelle //p':eval

Topics

versions

${task.process}:string

getorganelle_from_reads:string

get_organelle_from_reads.py --version 2>&1 | sed -n 's/GetOrganelle //p':eval

Tools

getorganelle GPL v3

maintainer

get in touch

`meta`
`:map`

`fastq`
`:file`

`organelle_type`
`:string`

`db`
`:directory`

`fasta`

`meta`
`:map`

`results/${prefix}.${organelle_type}.fasta.gz`
`:file`

`etc`

`results/*`
`:file`

`versions_getorganelle`

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

`getorganelle_from_reads`
`:string`

`get_organelle_from_reads.py --version 2>&1 | sed -n 's/GetOrganelle //p'`
`:eval`

`versions`

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

`getorganelle_from_reads`
`:string`

`get_organelle_from_reads.py --version 2>&1 | sed -n 's/GetOrganelle //p'`
`:eval`

getorganelle
GPL v3