Align short or PacBio reads to a reference genome using BBMap
Input
name:type
description
pattern
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
fastq{:bash}
:file
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
ref{:bash}
:file
Either “ref” a directory containing an index, the name of another directory
with a “ref” subdirectory containing an index or the name of a fasta formatted
nucleotide file containing the reference to map to.
Output
name:type
description
pattern
bam{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.bam{:bash}
:file
BAM file
*.{bam}
log{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.log{:bash}
:file
Log file
*.{log}
versions_bbmap{:bash}
${task.process}{:bash}
:string
The name of the process
bbmap{:bash}
:string
The name of the tool
bbversion.sh | grep -v "Duplicate cpuset"{:bash}
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions{:bash}
${task.process}{:bash}
:string
The name of the process
bbmap{:bash}
:string
The name of the tool
bbversion.sh | grep -v "Duplicate cpuset"{:bash}
:eval
The expression to obtain the version of the tool
Tools
bbmap
UC-LBL license (see package)
BBMap is a short read aligner, as well as various other bioinformatic tools.
