Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
input_files:file
BAM/CRAM file
*.{bam,cram,sam}
meta2:map
Groovy Map containing reference information
e.g. [ id:‘genome’ ]
fasta:file
Reference file the CRAM was created with (optional)
*.{fasta,fa}
meta3:map
Groovy Map containing reference information
e.g. [ id:‘genome’ ]
fai:file
Index of the reference file the CRAM was created with (optional)
*.fai
Output
name:type
description
pattern
bam
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
${prefix}.bam:file
BAM file
*.{bam}
cram
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
${prefix}.cram:file
CRAM file
*.{cram}
csi
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.csi:file
BAM index file (optional)
*.csi
crai
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.crai:file
CRAM index file (optional)
*.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.
