runsamplesheet.sh

Runs runsample on every sample/reference pair inside of a 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 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 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 graphs.sh)
  • Projects
    • All output from runsample placed under Projects named after each sample
  • QualDepth.pdf(See graphs.sh)
  • SampleCoverage.png(See graphs.sh)
  • vcf_consensus
    • Contains symbolic links(shortcuts) to each sample’s consensus.fasta file