Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
input_files{:bash}
:file
BAM/CRAM file
*.{bam,cram,sam}
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}
meta3{:bash}
:map
Groovy Map containing reference information
e.g. [ id:‘genome’ ]
fai{:bash}
:file
Index of the reference file the CRAM was created with (optional)
*.fai
meta4{:bash}
:map
Groovy Map containing reference information
e.g. [ id:‘genome’ ]
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{:bash}
versions.yml{:bash}
:file
File containing software versions
versions.yml
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.
