Description

Converts the contents of sequence data files (FASTA/FASTQ/SAM/BAM) into the RTG Sequence Data File (SDF) format.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

input1 (file)

FASTA, FASTQ, BAM or SAM file. This should be the left input file when using paired end FASTQ/FASTA data

*.{fasta,fa,fna,fastq,fastq.gz,fq,fq.gz,bam,sam}

input2 (file)

The right input file when using paired end FASTQ/FASTA data

*.{fasta,fa,fna,fastq,fastq.gz,fq,fq.gz}

sam_rg (file)

A file containing a single readgroup header as a SAM header. This can also be supplied as a string in task.ext.args as --sam-rg <rg_line>.

*.{txt,sam}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

sdf (directory)

The sequence dictionary format folder created from the input file(s)

*.sdf
included in
raredisease variantbenchmarking
maintainer
Github user nvnieuwk
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Tools

rtgtools
BSD

RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation

realtimegenomics.com/products/rtg-tools github.com/RealTimeGenomics/rtg-tools