modules/maltextract

Tool for evaluation of MALT results for true positives of ancient metagenomic taxonomic screening

maltMaltExtractHOPSalignmentmetagenomicsancient DNAaDNApalaeogenomicsarchaeogenomicsmicrobiomeauthenticationdamageedit distance

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

Description

Tool for evaluation of MALT results for true positives of ancient metagenomic taxonomic screening

Input

name:type

description

pattern

`meta`
`:map`

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

`rma6`
`:file`

RMA6 files from MALT

*.rma6

`taxon_list`
`:file`

List of target taxa to evaluate

*.txt

`ncbi_dir`
`:directory`

Directory containing NCBI taxonomy map and tre files

${ncbi_dir}/

Output

name:type

description

pattern

`results`

`meta`
`:directory`

Directory containing MaltExtract text results files

results/

`results`
`:directory`

Directory containing MaltExtract text results files

results/

`versions_maltextract`

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

The name of the process

`maltextract`
`:string`

The name of the tool

`MaltExtract --help | head -n 2 | tail -n 1 | sed 's/MaltExtract version//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`maltextract`
`:string`

The name of the tool

`MaltExtract --help | head -n 2 | tail -n 1 | sed 's/MaltExtract version//'`
`:eval`

The expression to obtain the version of the tool

Tools

maltextract
GPL 3

Java tool to work with ancient metagenomics

github.com/rhuebler/hops 10.1186/s13059-019-1903-0

modules/maltextract

Description

Input

`meta`
`:map`

`rma6`
`:file`

`taxon_list`
`:file`

`ncbi_dir`
`:directory`

Output

`results`

`meta`
`:directory`

`results`
`:directory`

`versions_maltextract`

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

`maltextract`
`:string`

`MaltExtract --help | head -n 2 | tail -n 1 | sed 's/MaltExtract version//'`
`:eval`

Topics

`versions`

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

`maltextract`
`:string`

`MaltExtract --help | head -n 2 | tail -n 1 | sed 's/MaltExtract version//'`
`:eval`

Tools

maltextract
GPL 3

maintainer

get in touch

modules/maltextract

Description

Input

meta :map

rma6 :file

taxon_list :file

ncbi_dir :directory

Output

results

meta :directory

results :directory

versions_maltextract

${task.process} :string

maltextract :string

MaltExtract --help | head -n 2 | tail -n 1 | sed 's/MaltExtract version//' :eval

Topics

versions

${task.process} :string

maltextract :string

MaltExtract --help | head -n 2 | tail -n 1 | sed 's/MaltExtract version//' :eval

Tools

maltextractGPL 3

maintainer

get in touch

`meta`
`:map`

`rma6`
`:file`

`taxon_list`
`:file`

`ncbi_dir`
`:directory`

`results`

`meta`
`:directory`

`results`
`:directory`

`versions_maltextract`

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

`maltextract`
`:string`

`MaltExtract --help | head -n 2 | tail -n 1 | sed 's/MaltExtract version//'`
`:eval`

`versions`

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

`maltextract`
`:string`

`MaltExtract --help | head -n 2 | tail -n 1 | sed 's/MaltExtract version//'`
`:eval`

maltextract
GPL 3