Description

Maps long reads to a metamaps database

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

reads:file

Input fastq file containing query sequences

*.{fq,fastq,fastq.gz,fq.gz}

database:file

Database file in fasta format

*.{fa,fasta}

Output

name:type
description
pattern

classification_res

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*classification_res:file

Coordinates where reads map

*.{classification_res}

meta_file

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*classification_res.meta:file

Statistics for mapping result

*.{classification_res.meta}

meta_unmappedreadsLengths

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*classification_res.meta.unmappedReadsLengths:file

Statistics for length of unmapped reads

*.{classification_res.meta.unmappedReadsLengths}

para_file

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*classification_res.parameters:file

Log with parameters

*.{classification_res.parameters}

versions

versions.yml:file

File containing software versions

versions.yml