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
sam
meta
:map
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
*.sam
:file
SAM file
*.sam
bam
meta
:map
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
*.bam
:file
Unaligned BAM file
*.bam
cram
meta
:map
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
*.cram
:file
Unaligned CRAM file
*.cram
versions_samtools
${task.process}
:string
The process the versions were collected from
samtools
:string
The tool name
samtools version | sed '1!d;s/.* //'
:string
The command used to generate the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
The process the versions were collected from
samtools
:string
The tool name
samtools version | sed '1!d;s/.* //'
: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.
