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¶
Generate your custom config.yaml
make_example_config
Edit the config.yaml generated to suit your needs
Run
runsamplesheet.sh
with custom config.yamlRUNSAMPLEOPTIONS="-c config.yaml" runsamplesheet.sh /path/to/ReadsBySample /path/to/samplesheet.tsv
Creates¶
- graphsample.log
- Logfile from running
graphsample
on all samples in samplesheet
- Logfile from running
- 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
- All output from
QualDepth.pdf(See graphs.sh)
SampleCoverage.png(See graphs.sh)
- vcf_consensus
- Contains symbolic links(shortcuts) to each sample’s consensus.fasta file