Assembles a small genome (bacterial, fungal, viral)
Input
name:type
description
pattern
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
illumina
:file
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
:file
List of input PacBio CLR FastQ files of size 1.
nanopore
:file
List of input FastQ files of size 1, originating from Oxford Nanopore technology.
yml
:file
Path to yml file containing read information.
The raw FASTQ files listed in this YAML file MUST be supplied to the respective illumina/pacbio/nanopore input channel(s) in addition to this YML.
File entries in this yml must contain only the file name and no paths.
*.{yml,yaml}
hmm
:file
File or directory with amino acid HMMs for Spades HMM-guided mode.
Output
name:type
description
pattern
scaffolds
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.fa.gz
*.scaffolds.fa.gz
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.fa.gz
contigs
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.fa.gz
*.contigs.fa.gz
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.fa.gz
transcripts
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.fa.gz
*.transcripts.fa.gz
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.fa.gz
gene_clusters
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.fa.gz
*.gene_clusters.fa.gz
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.fa.gz
gfa
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.fa.gz
*.assembly.gfa.gz
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.gfa.gz
warnings
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.fa.gz
*.warnings.log
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
log
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.fa.gz
*.spades.log
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.spades.log
versions_spades
${task.process}
:string
The process the versions were collected from
spades
:string
The tool name
spades.py --version 2>&1 | sed -n 's/^.*SPAdes genome assembler v//p'
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
The name of the process
spades
:string
The name of the tool
spades.py --version 2>&1 | sed -n 's/^.*SPAdes genome assembler v//p'
:eval
The expression to obtain the version of the tool
Tools
spades
GPL v2
SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.
