runsamplesheet.rst

orphan:

runsamplesheet.sh

Runs :py:mod:`runsample <ngs_mapper.runsample>` on every sample/reference pair inside of a :doc:`../samplesheet`

Usage

runsamplesheet.sh /path/to/ReadsBySample /path/to/samplesheet.tsv

Passing options to runsample

You can run runsamplesheet.sh and pass arguments to runsample by prepending RUNSAMPLEOPTIONS="" to the command

Example: adding -minth option

This would run each sample and pass "-minth 0.95" to :py:mod:`runsample <ngs_mapper.runsample>`

RUNSAMPLEOPTIONS="-minth 0.95" runsamplesheet.sh /path/to/ReadsBySample /path/to/samplesheet.tsv

Example: Supplying custom config.yaml file

1. Generate your custom config.yaml

   make_example_config

2. Edit the config.yaml generated to suit your needs

3. Run runsamplesheet.sh with custom config.yaml

   RUNSAMPLEOPTIONS="-c config.yaml" runsamplesheet.sh /path/to/ReadsBySample /path/to/samplesheet.tsv

Creates

• graphsample.log

  • Logfile from running :py:mod:`graphsample <ngs_mapper.graphsample>` on all samples in samplesheet

• MapUnmapReads.png

  • Graphic that shows each sample's mapped vs unmapped read counts

• pipeline.log

  • Logfile that contains essentially the same information on the console you get when you run runsample except it also includes debug lines

• PipelineTimes.png(See :doc:`graphs`)

• Projects

  • All output from :py:mod:`runsample <ngs_mapper.runsample>` placed under Projects named after each sample

• QualDepth.pdf(See :doc:`graphs`)
• SampleCoverage.png(See :doc:`graphs`)

• vcf_consensus

  • Contains symbolic links(shortcuts) to each sample's consensus.fasta file