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