Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
input:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
index:file
BAM.BAI/BAM.CSI/CRAM.CRAI file (optional)
*.{.bai,.csi,.crai}
meta2:map
Groovy Map containing reference information
e.g. [ id:‘test’ ]
fasta:file
Reference file the CRAM was created with (optional)
*.{fasta,fa}
qname:file
Optional file with read names to output only select alignments
*.{txt,list}
index_format:string
Index format, used together with ext.args = ‘—write-index’
bai|csi|crai
Output
name:type
description
pattern
bam
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
${prefix}.bam:file
optional filtered/converted BAM file
*.{bam}
cram
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
${prefix}.cram:file
optional filtered/converted CRAM file
*.{cram}
sam
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
${prefix}.sam:file
optional filtered/converted SAM file
*.{sam}
bai
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
${prefix}.${file_type}.bai:file
optional BAM file index
*.{bai}
csi
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
${prefix}.${file_type}.csi:file
optional tabix BAM file index
*.{csi}
crai
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
${prefix}.${file_type}.crai:file
optional CRAM file index
*.{crai}
unselected
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
${prefix}.unselected.${file_type}:file
optional file with unselected alignments
*.unselected.{bam,cram,sam}
unselected_index
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
${prefix}.unselected.${file_type}.{csi,crai}:file
index for the “unselected” file
*.unselected.{csi,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.
