Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
input_files{:bash}
:file
BAM/CRAM files
*.{bam,cram}
Output
name:type
description
pattern
bam{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.bam{:bash}
:file
Concatenated BAM file
*.{bam}
cram{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.cram{:bash}
:file
Concatenated CRAM file
*.{cram}
versions_samtools{:bash}
${task.process}{:bash}
:string
The name of the process
samtools{:bash}
:string
The name of the tool
samtools version | sed '1!d;s/.* //'{:bash}
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions{:bash}
${task.process}{:bash}
:string
The name of the process
samtools{:bash}
:string
The name of the tool
samtools version | sed '1!d;s/.* //'{:bash}
:eval
The expression to obtain 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.
