Description

mark duplicate alignments in a coordinate sorted file

Input

Name (Type)
Description
Pattern

meta (map)

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

]

input (file)

BAM/CRAM/SAM file

*.{bam,cram,sam}

fasta (file)

A reference genome in FASTA format

*.fasta

meta2 (map)

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

]

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

output (file)

Sorted BAM/CRAM/SAM file

*.{bam,cram,sam}
maintainer
Github user priyanka-surana
get in touch
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