Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
reads{:bash}
:file
fastq data to be converted to SAM/BAM/CRAM
*.{fastq,fq,fastq.gz,fq.gz}
Output
name:type
description
pattern
sam{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
*.sam{:bash}
:file
SAM file
*.sam
bam{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
*.bam{:bash}
:file
Unaligned BAM file
*.bam
cram{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
*.cram{:bash}
:file
Unaligned CRAM file
*.cram
versions{:bash}
versions.yml{:bash}
:file
File containing software versions
versions.yml
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.
