Description

Converts a FASTQ file to an unaligned BAM or SAM file.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

reads (file)

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

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

bam (file)

Unaligned bam file

*.{bam}
author
Github user matthdsm
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

picard
MIT

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

broadinstitute.github.io/picard gatk.broadinstitute.org/hc/en-us/articles/360036510672-FastqToSam-Picard- https://github.com/broadinstitute/picard