Align short or PacBio reads to a reference genome using BBMap
Input
name:type
description
pattern
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
fastq
:file
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
ref
: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
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.bam
:file
BAM file
*.{bam}
log
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.log
:file
Log file
*.{log}
versions_bbmap
${task.process}
:string
The name of the process
bbmap
:string
The name of the tool
bbversion.sh | grep -v "Duplicate cpuset"
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
The name of the process
bbmap
:string
The name of the tool
bbversion.sh | grep -v "Duplicate cpuset"
: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.
