modules/last_train

Find suitable score parameters for sequence alignment

LASTtrainfastqfasta

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

Description

Find suitable score parameters for sequence alignment

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`fastx`
`:file`

FASTA/FASTQ file

*.{fasta,fastq}

`index`
`:directory`

Directory containing the files of the LAST index

lastdb/

Output

name:type

description

pattern

`param_file`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`*.train`
`:file`

Trained parameter file

*.train

`multiqc`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`*.tsv`
`:file`

Alignment parameter summary for MultiQC

*.tsv

`versions_last`

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

The name of the process

`last`
`:string`

The name of the tool

`lastal --version | sed 's/lastal //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`last`
`:string`

The name of the tool

`lastal --version | sed 's/lastal //'`
`:eval`

The expression to obtain the version of the tool

Tools

last
GPL v3-or-later

LAST finds & aligns related regions of sequences.

gitlab.com/mcfrith/last gitlab.com/mcfrith/last/-/blob/main/doc/last-train.rst https://gitlab.com/mcfrith/last

modules/last_train

Description

Input

`meta`
`:map`

`fastx`
`:file`

`index`
`:directory`

Output

`param_file`

`meta`
`:map`

`*.train`
`:file`

`multiqc`

`meta`
`:map`

`*.tsv`
`:file`

`versions_last`

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

`last`
`:string`

`lastal --version | sed 's/lastal //'`
`:eval`

Topics

`versions`

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

`last`
`:string`

`lastal --version | sed 's/lastal //'`
`:eval`

Tools

last
GPL v3-or-later

included in

maintainer

get in touch

modules/last_train

Description

Input

meta :map

fastx :file

index :directory

Output

param_file

meta :map

*.train :file

multiqc

meta :map

*.tsv :file

versions_last

${task.process} :string

last :string

lastal --version | sed 's/lastal //' :eval

Topics

versions

${task.process} :string

last :string

lastal --version | sed 's/lastal //' :eval

Tools

lastGPL v3-or-later

included in

maintainer

get in touch

`meta`
`:map`

`fastx`
`:file`

`index`
`:directory`

`param_file`

`meta`
`:map`

`*.train`
`:file`

`multiqc`

`meta`
`:map`

`*.tsv`
`:file`

`versions_last`

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

`last`
`:string`

`lastal --version | sed 's/lastal //'`
`:eval`

`versions`

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

`last`
`:string`

`lastal --version | sed 's/lastal //'`
`:eval`

last
GPL v3-or-later