Identify insertion sites positions in bacterial genomes
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
reads
:file
A set of paired-end FASTQ files
*.{fastq.gz,fq.gz}
reference
Reference genome in GenBank format
*.{gbk}
query
Insertion sequences to query in FASTA format
*.{fasta,fa}
results
results/*
:directory
Directory containing ISMapper result files
*/*
versions_ismapper
${task.process}
:string
The name of the process
ismapper
The name of the tool
ismap --version 2>&1 | sed -n 's/^.*ismap //p'
:eval
The expression to obtain the version of the tool
versions
A mapping-based tool for identification of the site and orientation of IS insertions in bacterial genomes.
