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{:bash}

:map

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

input1{:bash}

: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{:bash}

:file

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

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

sam_rg{:bash}

: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{:bash}

meta{:bash}

:map

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

*.sdf{:bash}

:directory

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

*.sdf

versions_rtgtools{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

rtgtools{:bash}

:string

The name of the tool

rtg version | head -n 1 | sed 's/Product: RTG Tools //'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

rtgtools{:bash}

:string

The name of the tool

rtg version | head -n 1 | sed 's/Product: RTG Tools //'{:bash}

:eval

The expression to obtain the version of the tool

Tools

included in
rarediseasevariantbenchmarking
maintainer
Github user nvnieuwk
get in touch
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