modules/malt_run

MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics.

maltalignmentmetagenomicsancient DNAaDNApalaeogenomicsarchaeogenomicsmicrobiome

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

Description

MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics.

Input

name:type

description

pattern

`meta`
`:map`

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

`fastqs`
`:file`

Input FASTQ files

*.{fastq.gz,fq.gz}

`meta2`
`:map`

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

`index`
`:directory`

Index/database directory from malt-build

*/

Output

name:type

description

pattern

`rma6`

`meta`
`:file`

MEGAN6 RMA6 file

*.rma6

`*.rma6`
`:file`

MEGAN6 RMA6 file

*.rma6

`alignments`

`meta`
`:file`

MEGAN6 RMA6 file

*.rma6

`*.{tab,text,sam,tab.gz,text.gz,sam.gz}`
`:file`

Alignment files in Tab, Text or MEGAN-compatible SAM format

*.{tab,txt,sam}

`log`

`meta`
`:file`

MEGAN6 RMA6 file

*.rma6

`*.log`
`:file`

Log of verbose MALT stdout

*-malt-run.log

`versions_malt`

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

The name of the process

`malt`
`:string`

The name of the tool

`malt-run --help |& sed '/version/!d;s/.version //;s/,.//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`malt`
`:string`

The name of the tool

`malt-run --help |& sed '/version/!d;s/.version //;s/,.//'`
`:eval`

The expression to obtain the version of the tool

Tools

malt
GPL v3

A tool for mapping metagenomic data

wsi.uni-tuebingen.de/lehrstuehle/algorithms-in-bioinformatics/software/malt software-ab.cs.uni-tuebingen.de/download/malt/manual.pdf 10.1038/s41559-017-0446-6

modules/malt_run

Description

Input

`meta`
`:map`

`fastqs`
`:file`

`meta2`
`:map`

`index`
`:directory`

Output

`rma6`

`meta`
`:file`

`*.rma6`
`:file`

`alignments`

`meta`
`:file`

`*.{tab,text,sam,tab.gz,text.gz,sam.gz}`
`:file`

`log`

`meta`
`:file`

`*.log`
`:file`

`versions_malt`

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

`malt`
`:string`

`malt-run --help |& sed '/version/!d;s/.version //;s/,.//'`
`:eval`

Topics

`versions`

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

`malt`
`:string`

`malt-run --help |& sed '/version/!d;s/.version //;s/,.//'`
`:eval`

Tools

malt
GPL v3

included in

maintainer

get in touch

modules/malt_run

Description

Input

meta :map

fastqs :file

meta2 :map

index :directory

Output

rma6

meta :file

*.rma6 :file

alignments

meta :file

*.{tab,text,sam,tab.gz,text.gz,sam.gz} :file

log

meta :file

*.log :file

versions_malt

${task.process} :string

malt :string

malt-run --help |& sed '/version/!d;s/.*version //;s/,.*//' :eval

Topics

versions

${task.process} :string

malt :string

malt-run --help |& sed '/version/!d;s/.*version //;s/,.*//' :eval

Tools

maltGPL v3

included in

maintainer

get in touch

`meta`
`:map`

`fastqs`
`:file`

`meta2`
`:map`

`index`
`:directory`

`rma6`

`meta`
`:file`

`*.rma6`
`:file`

`alignments`

`meta`
`:file`

`*.{tab,text,sam,tab.gz,text.gz,sam.gz}`
`:file`

`log`

`meta`
`:file`

`*.log`
`:file`

`versions_malt`

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

`malt`
`:string`

`malt-run --help |& sed '/version/!d;s/.version //;s/,.//'`
`:eval`

`versions`

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

`malt`
`:string`

`malt-run --help |& sed '/version/!d;s/.version //;s/,.//'`
`:eval`

malt
GPL v3