Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
input_files{:bash}
:file
BAM/CRAM file
*.{bam,cram,sam}
index_files{:bash}
:file
BAI/CRAI/CSI index file
*.{bai,crai,csi}
meta2{:bash}
:map
Groovy Map containing reference information
e.g. [ id:‘genome’ ]
fasta{:bash}
:file
Reference file the CRAM was created with (optional)
*.{fasta,fa}
fai{:bash}
:file
Index of the reference file the CRAM was created with (optional)
*.fai
gzi{:bash}
:file
Index of the compressed reference file the CRAM was created with (optional)
*.gzi
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
BAM file
*.{bam}
cram{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.cram{:bash}
:file
CRAM file
*.{cram}
csi{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.csi{:bash}
:file
BAM index file (optional)
*.csi
crai{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.crai{:bash}
:file
CRAM index file (optional)
*.crai
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.
