nf-core_modules/modules/spades/meta.yml

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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 ]
- illumina:
type: file
description: |
List of input FastQ (Illumina or PacBio CCS reads) files
of size 1 and 2 for single-end and paired-end data,
respectively. This input data type is required.
- pacbio:
type: file
description: |
List of input PacBio CLR FastQ files of size 1.
- nanopore:
type: file
description: |
List of input FastQ files of size 1, originating from Oxford Nanopore technology.
- 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
pattern: "*.fa.gz"
- contigs:
type: file
description: |
Fasta file containing contigs
pattern: "*.fa.gz"
- transcripts:
type: file
description: |
Fasta file containing transcripts
pattern: "*.fa.gz"
- gene_clusters:
type: file
description: |
Fasta file containing gene_clusters
pattern: "*.fa.gz"
- gfa:
type: file
description: |
gfa file containing assembly
pattern: "*.gfa.gz"
- log:
type: file
description: |
Spades log file
pattern: "*.log"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@JoseEspinosa"
- "@drpatelh"
- "@d4straub"