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_samtools{:bash}
${task.process}{:bash}
:string
The process the versions were collected from
samtools{:bash}
:string
The tool name
samtools version | sed '1!d;s/.* //'{:bash}
:string
The command used to generate the version of the tool
Topics
name:type
description
pattern
versions{:bash}
${task.process}{:bash}
:string
The process the versions were collected from
samtools{:bash}
:string
The tool name
samtools version | sed '1!d;s/.* //'{:bash}
:string
The command used to generate the version of the tool
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.
