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