Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
input_files{:bash}
:file
BAM/CRAM files
*.{bam,cram}
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
Concatenated BAM file
*.{bam}
cram{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.cram{:bash}
:file
Concatenated CRAM file
*.{cram}
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.
