recipe biopet-sampleconfig

#### Tools - ExtractTsv This mean can extract samples, libraries and readgroups from a sample config file.

Homepage

https://github.com/biopet/sampleconfig

License

MIT

Recipe

/biopet-sampleconfig/meta.yaml

#### Tools - ExtractTsv

This mean can extract samples, libraries and readgroups from a sample config file. This meant as a supporting tool inside wdl pipelines. It can also output a single layer as tsv file.

#### Tools - ReadFromTsv

This tool enables a user to create a full sample sheet in JSON format or YAML format, suitable for all Biopet Queue pipelines, from TSV file(s).

#### Tools - CromwellArrays

This tool will convert the sample configs to a array based format that can be used inside wdl pipelines. This tool is only to support biowdl pipelines.

#### Tools - CaseControl

This tool will extract the case-control pairs from a sample config file. It will read the headers of the bam files to confirm that samples do exist.

For documentation and manuals visit our github.io page: https://biopet.github.io/sampleconfig

package biopet-sampleconfig

(downloads) docker_biopet-sampleconfig

Versions

0.3-00.2-00.1-10.1-0

Depends
Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install biopet-sampleconfig

and update with:

conda update biopet-sampleconfig

or use the docker container:

docker pull quay.io/biocontainers/biopet-sampleconfig:<tag>

(see biopet-sampleconfig/tags for valid values for <tag>)

Notes

biopet-sampleconfig is a Java program that comes with a custom wrapper shell script. By default 'no default java option' is set in the wrapper. The command that runs the program is 'biopet-sampleconfig'. If you want to overwrite it you can specify memory options directly after your binaries. If you have _JAVA_OPTIONS set globally this will take precedence. For example run it with 'biopet-sampleconfig -Xms512m -Xmx1g'.