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).
