Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
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:‘genome’ ]
fasta
:file
Fasta reference file
*.{fasta,fa}
fai
:file
Fasta reference file index
*.{fai}
meta3
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
qname
:file
Optional file with read names to output only select alignments
*.{txt,list}
meta4
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
bed
:file
Optional BED file for filtering alignments by genomic region (-L)
*.{bed}
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:false ]
${prefix}.bam
:file
optional filtered/converted BAM file
*.{bam}
cram
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.cram
:file
optional filtered/converted CRAM file
*.{cram}
sam
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.sam
:file
optional filtered/converted SAM file
*.{sam}
bai
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.${file_type}.bai
:file
optional BAM file index
*.{bai}
csi
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.${file_type}.csi
:file
optional tabix BAM file index
*.{csi}
crai
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.${file_type}.crai
:file
optional CRAM file index
*.{crai}
unselected
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.unselected.${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:false ]
${prefix}.unselected.${file_type}.{csi,crai}
:file
index for the “unselected” file
*.unselected.{csi,crai}
versions_samtools
${task.process}
:string
Name of the process
samtools
:string
Name of the tool
samtools version | sed "1!d;s/.* //"
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
Name of the process
samtools
:string
Name of the tool
samtools version | sed "1!d;s/.* //"
:eval
The expression to obtain the version of the tool
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.
