Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
input
:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
interleave
:boolean
Set true for interleaved fastq file
Output
name:type
description
pattern
fastq
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*_{1,2}.fastq.gz
:file
Compressed FASTQ file(s) with reads with either the READ1 or READ2 flag set in separate files.
*_{1,2}.fastq.gz
interleaved
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*_interleaved.fastq
:file
Compressed FASTQ file with reads with either the READ1 or READ2 flag set in a combined file. Needs collated input file.
*_interleaved.fastq.gz
singleton
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*_singleton.fastq.gz
:file
Compressed FASTQ file with singleton reads
*_singleton.fastq.gz
other
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*_other.fastq.gz
:file
Compressed FASTQ file with reads with either both READ1 and READ2 flags set or unset
*_other.fastq.gz
versions_samtools
${task.process}
:string
The name of the process
samtools
:string
The 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
The name of the process
samtools
:string
The 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.
