Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
bam
:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
meta2
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
fasta
:file
FASTA ref file
*.{fasta,fa,fna}
fai
:file
FASTA ref index file
*.{fasta,fa,fna}.fai
Output
name:type
description
pattern
bam
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.bam
:file
Sorted BAM/CRAM/SAM file
*.{bam,cram,sam}
versions_samtools
${task.process}
:string
The name of the process
samtools
:string
The name of the tool
samtools version | sed '1!d;s/.* //'
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
The name of the process
samtools
:string
The name of the tool
samtools version | sed '1!d;s/.* //'
:eval
The expression to obtain the version of the tool
Tools
samtoolscalmd
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.
