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

sdf

meta:map

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

]

*.sdf:directory

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

*.sdf

versions

versions.yml:file

File containing software versions

versions.yml

Tools

rtgtools
BSD

RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation