nf-core_modules/modules/epang/meta.yml
Daniel Lundin e97d4cd32b
epang: Output gzipped jplace (#2037)
* Output gzipped jplace
2022-09-09 09:54:03 +02:00

70 lines
2 KiB
YAML

name: "epang"
description: phylogenetic placement of query sequences in a reference tree
keywords:
- phylogeny
- phylogenetic placement
- sequences
tools:
- "epang":
description: "Massively parallel phylogenetic placement of genetic sequences"
homepage: "https://github.com/Pbdas/epa-ng"
documentation: "https://github.com/Pbdas/epa-ng/wiki/Full-Stack-Example"
tool_dev_url: "https://github.com/Pbdas/epa-ng"
doi: "https://doi.org/10.1093/sysbio/syy054"
licence: "['GNU Affero General Public License v3.0']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test' ]
- queryaln:
type: file
description: aligned query sequences in any supported format including phylip and fasta, may be gzipped
pattern: "*"
- referencealn:
type: file
description: reference alignment in any supported format including phylip and fasta, may be gzipped
pattern: "*"
- referencetree:
type: file
description: newick file containing the reference tree in which query sequences will be placed
pattern: "*"
- bfastfile:
type: file
description: file argument to the --bfast parameter
pattern: "*"
- splitfile:
type: file
description: file argument to the --split parameter
pattern: "*"
- binaryfile:
type: file
description: file argument to the --binary parameter
pattern: "*"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test' ]
- epang:
type: directory
description: directory in which EPA-NG was run
- jplace:
type: file
description: gzipped file with placement information
pattern: "*.jplace.gz"
- log:
type: file
description: log file from placement
pattern: "*.log"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@erikrikarddaniel"