modules/malt_build

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 DNAaDNApalaeogenomicsarchaeogenomicsmicrobiomedatabase

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

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

`fastas:file`

Directory of, or list of FASTA reference files for indexing

*/|*.fasta

`gff:file`

Directory of, or GFF3 files of input FASTA files

*/|*.gff|*.gff3

`mapping_db:file`

An uncompressed MEGAN mapping file from https://software-ab.cs.uni-tuebingen.de/download/megan6/welcome.html (either mapping db, or acc2*..abin file)

*.{db,abin}

`map_type:string`

The type of map file provided to the pipeline. Must be a valid string corresponding to a single-dash parameter, for example ‘-a2tax’ or ‘-a2interpro2go’

mdb|a2t|s2t|a2ec|s2ec|t4ec|a2eggnog|s2eggnog|t4eggnog|a2gtdb|s2gtdb|t4gtdb|a2interpro2go|s2interpro2go|t4interprotogo|a2kegg|s2kegg|t4kegg|a2pgpt|s2pgpt|t4pgpt|a2seed|s2seed|t4seed

Output

name:type

description

pattern

`index`

`malt_index/:directory`

Directory containing MALT database index directory

malt_index/

`versions`

`versions.yml:file`

File containing software versions

versions.yml

`log`

`malt-build.log:file`

Log file from STD out of malt-build

malt-build.log

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_build

Description

Input

fastas:file

gff:file

mapping_db:file

map_type:string

Output

index

malt_index/:directory

versions

versions.yml:file

log

malt-build.log:file