Description

Assembly polisher using short (and long) reads

Input

Name (Type)
Description
Pattern

meta (map)

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

]

reads (file)

Short reads file(s). In fastq or fasta, compressed or uncompressed

meta2 (map)

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

]

sr_bam (file)

Aligned short-read BAM/SAM file. Must have CIGAR information.

*.{bam,sam}

draft (file)

Input (fasta) file containing draft contig assembly

genome_size (string)

Estimated size of the genome. Number or nts or use suffixes k/m/g, e.g. 5m, 3.2g

reads_coverage (integer)

Appprimate depth of coverage of short reads.

Output

Name (Type)
Description
Pattern

meta (map)

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

]

fasta (file)

Polished assembly fasta file

*.fasta

versions (file)

File containing software versions

versions.yml