convert and then index CRAM -> BAM or BAM -> CRAM file
Input
name:type
description
pattern
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
input{:bash}
:file
BAM/CRAM file
*.{bam,cram}
index{:bash}
:file
BAM/CRAM index file
*.{bai,crai}
meta2{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
fasta{:bash}
:file
Reference file to create the CRAM file
*.{fasta,fa}
meta3{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
fai{:bash}
:file
Reference index file to create the CRAM file
*.{fai}
Output
name:type
description
pattern
bam{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.bam{:bash}
:file
filtered/converted BAM file
*{.bam}
cram{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.cram{:bash}
:file
filtered/converted CRAM file
*{cram}
bai{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.bai{:bash}
:file
filtered/converted BAM index
*{.bai}
crai{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.crai{:bash}
:file
filtered/converted CRAM index
*{.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.
