Description

Aligns query sequences to target sequences indexed with lastdb

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

fastx:file

FASTA/FASTQ file

*.{fasta,fastq}

param_file:file

Trained parameter file

*.train

index:directory

Directory containing the files of the LAST index

lastdb/

Output

name:type
description
pattern

maf

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.maf.gz:file

Gzipped MAF (Multiple Alignment Format) file

*.{maf.gz}

multiqc

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.tsv:file

Summary reporting the total alignment length (including gaps) and the percent identity computed with and without taking gaps in consideration (because there is no standard definition of percent identity).

*.tsv

versions

versions.yml:file

File containing software versions

versions.yml