Description

converts FASTQ files to unmapped SAM/BAM/CRAM

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]

reads (file)

fastq data to be converted to SAM/BAM/CRAM

*.{fastq,fq,fastq.gz,fq.gz}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]

versions (file)

File containing software versions

versions.yml

sam (file)

SAM file

*.sam

bam (file)

Unaligned BAM file

*.bam

cram (file)

Unaligned CRAM file

*.cram
author
Github user matthdsm
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Tools

samtools
MIT

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

http://www.htslib.org http://www.htslib.org/doc/samtools 10.1093/bioinformatics/btp352