Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
bam
:file
BAM file
*.{bam}
meta2
:map
Groovy Map containing sample information about the reference fasta
e.g. [ id:‘reference’ ]
fasta
:file
Reference genome FASTA file
*.{fasta,fa}
Output
name:type
description
pattern
bam
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.bam
:file
BAM file with indel qualities inserted into it
*.{bam}
versions_lofreq
${task.process}
:string
Process which generated the version
lofreq
:string
Tool name
lofreq version | sed -n '1s/^.* //p'
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
Process which generated the version
lofreq
:string
Tool name
lofreq version | sed -n '1s/^.* //p'
:eval
The expression to obtain the version of the tool
Tools
lofreq
MIT
Lofreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It's indelqual programme inserts indel qualities in a BAM file
