mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-27 15:53:16 -05:00
70 lines
1.8 KiB
YAML
70 lines
1.8 KiB
YAML
|
name: spades
|
||
|
|
description: Assembles a small genome (bacterial, fungal, viral)
|
||
|
|
keywords:
|
||
|
|
- genome
|
||
|
|
- assembly
|
||
|
|
- genome assembler
|
||
|
|
- small genome
|
||
|
|
- de novo assembler
|
||
|
|
tools:
|
||
|
|
- spades:
|
||
|
|
description: SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.
|
||
|
|
homepage: http://cab.spbu.ru/files/release3.15.0/manual.html
|
||
|
|
documentation: http://cab.spbu.ru/files/release3.15.0/manual.html
|
||
|
|
tool_dev_url: https://github.com/ablab/spades
|
||
|
|
doi: 10.1089/cmb.2012.0021
|
||
|
|
licence: ['GPL v2']
|
||
|
|
input:
|
||
|
|
- meta:
|
||
|
|
type: map
|
||
|
|
description: |
|
||
|
|
Groovy Map containing sample information
|
||
|
|
e.g. [ id:'test', single_end:false ]
|
||
|
|
- reads:
|
||
|
|
type: file
|
||
|
|
description: |
|
||
|
|
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||
|
|
respectively.
|
||
|
|
- hmm:
|
||
|
|
type: file
|
||
|
|
description:
|
||
|
|
File or directory with amino acid HMMs for Spades HMM-guided mode.
|
||
|
|
output:
|
||
|
|
- meta:
|
||
|
|
type: map
|
||
|
|
description: |
|
||
|
|
Groovy Map containing sample information
|
||
|
|
e.g. [ id:'test', single_end:false ]
|
||
|
|
- scaffolds:
|
||
|
|
type: file
|
||
|
|
description: |
|
||
|
|
Fasta file containing scaffolds
|
||
|
|
- contigs:
|
||
|
|
type: file
|
||
|
|
description: |
|
||
|
|
Fasta file containing contigs
|
||
|
|
- transcripts:
|
||
|
|
type: file
|
||
|
|
description: |
|
||
|
|
Fasta file containing transcripts
|
||
|
|
- gene_clusters:
|
||
|
|
type: file
|
||
|
|
description: |
|
||
|
|
Fasta file containing gene_clusters
|
||
|
|
- gfa:
|
||
|
|
type: file
|
||
|
|
description: |
|
||
|
|
gfa file containing assembly
|
||
|
|
- log:
|
||
|
|
type: file
|
||
|
|
description: |
|
||
|
|
Spades log file
|
||
|
|
- version:
|
||
|
|
type: file
|
||
|
|
description: File containing software version
|
||
|
|
pattern: "*.{version.txt}"
|
||
|
|
|
||
|
|
authors:
|
||
|
|
- "@JoseEspinosa"
|
||
|
|
- "@drpatelh"
|