Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
bam:file
BAM/CRAM/SAM file(s)
*.{bam,cram,sam}
meta2:map
Groovy Map containing reference information
e.g. [ id:‘genome’ ]
fasta:file
Reference genome FASTA file
*.{fa,fasta,fna}
Output
name:type
description
pattern
bam
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.bam:file
Sorted BAM file
*.{bam}
cram
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.cram:file
Sorted CRAM file
*.{cram}
crai
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.crai:file
CRAM index file (optional)
*.crai
csi
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.csi:file
BAM index file (optional)
*.csi
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.
