Description

Post-processing script of the MaltExtract component of the HOPS package

Input

name:type
description
pattern

maltextract_results{:bash}

:directory

MaltExtract output directory

results/

taxon_list{:bash}

:file

List of target taxa to evaluate used in MaltExtract

*.txt

filter{:bash}

:string

The filter mode used in MaltExtract

def_anc|default|scan|ancient|crawl

Output

name:type
description
pattern

json{:bash}

results/heatmap_overview_Wevid.json{:bash}

:file

Candidate summary heatmap in MultiQC compatible JSON format

heatmap_overview_Wevid.json

summary_pdf{:bash}

results/heatmap_overview_Wevid.pdf{:bash}

:file

Candidate summary heatmap in PDF format

heatmap_overview_Wevid.pdf

tsv{:bash}

results/heatmap_overview_Wevid.tsv{:bash}

:file

Candidate summary heatmap in TSV format

heatmap_overview_Wevid.tsv

candidate_pdfs{:bash}

results/pdf_candidate_profiles/{:bash}

:directory

Directory of per sample output PDFs organised by reference

pdf_candidate_profiles/

versions_hops{:bash}

${task.process}{:bash}

:string

The name of the process

hops{:bash}

:string

The name of the tool

hops --version 2>&1 | sed 's/HOPS version//' {:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

hops{:bash}

:string

The name of the tool

hops --version 2>&1 | sed 's/HOPS version//' {:bash}

:eval

The expression to obtain the version of the tool

Tools

amps
GPL >=3

Post-processing script of the MaltExtract tool for ancient metagenomics

github.com/rhuebler/HOPS github.com/keyfm/amps 10.1186/s13059-019-1903-0
maintainer
Github user jfy133
get in touch
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