Description

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}

fasta (file)

Reference file to create the CRAM file

*.{fasta,fa}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]

alignment_index (file)

filtered/converted BAM/CRAM file + index

*{.bam/cram,.bai/crai}

version (file)

File containing software version

*.{version.txt}

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.