nf-core_modules/software/spades/meta.yml
Jose Espinosa-Carrasco 72e81d6e90
Add spades module (#277)
* Add spades module

* Reorder gatk4 modules alphabetically

* Update software/spades/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-18 13:48:38 +00:00

74 lines
2 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.
- coronaspades:
type: boolean
description: |
Run coronaspades instead of default spades mode. coronaSPAdes is a special
mode of rnaviralSPAdes specifically aimed for SARS-CoV-2 de novo assembly.
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"