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
Input FastQ files: one file for single-end data, and two files, or one
interleaved file, for paired-end data.
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_format
:string
Format of the output reads, one of “bam”, “fastq”, “fastq.gz”, “fasta” or
“fasta.gz”. Defaults to “bam” if empty.
output_reads
:string
Which reads to write, one of “all” (bbmap out), “mapped” (outm) or
“unmapped” (outu). Defaults to “all” if empty.
interleaved_output
:boolean
Whether to write paired-end fastq/fasta output to a single interleaved
file instead of two files. Has no effect on single-end or bam output.
Output
name:type
description
pattern
bam
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.bam
:file
BAM file, written when output_format is “bam”. Named ${prefix}.bam
for all reads, ${prefix}.<output_reads>.bam otherwise.
*.{bam}
reads
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.{fastq,fastq.gz,fasta,fasta.gz}
:file
Reads in fastq/fasta format, written when output_format is not “bam” and
named ${prefix}.<output_reads>. Paired-end reads are split into _1 and
_2 files unless interleaved_output is true.
*.{fastq,fastq.gz,fasta,fasta.gz}
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.
