Description

Align fastq files to a reference genome

Input

name:type
description
pattern

meta :map

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

reads :file

List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.

meta2 :map

Groovy Map containing reference information
e.g. [ id:‘test’ ]

index :file

Aligner genome index files

Directory containing aligner index

meta3 :map

Groovy Map containing reference information
e.g. [ id:‘genome’ ]

fasta :file

Reference genome in fasta format

*.{fa, fasta, fna}

aligner :string

Aligner to use for alignment

sort_bam :boolean

sort output

Output

name:type
description
pattern

meta :map

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

bam :file

BAM file

*.bam

bam_index :file

BAM index (currently only for snapaligner)

*.{bai, csi}

report :file

Alignment report (currently only for dragmap)

*.txt

versions :file

File containing software versions

versions.yml