03. Example Data

Content and Options

The example data holds a toy dataset (reduced read files, 25 target loci) for 4 samples.

You can run the example data to test your system setup either by

1. following the instructions in the Quick-Start guide which automatically runs the example based on the Nextflow -profile test
2. following the instructions below by using local data files

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Running the Example Locally

To run the example data

1. follow the nextflow and pipesnake installation instructions in the Quick-Start guide
2. make sure to change file paths in the ToyData_SampleInfo.csv file to direct to the read files (full paths within your working directory).
3. run the example analysis with read filtering:

nextflow run pipesnake/ --input pipesnake/example/data/ToyData_SampleInfo.csv --outdir pipesnake/TEST2 --blat_db pipesnake/example/data/ToyData_SqCL_25Targets.fasta --filter pipesnake/example/data/ToyData_SqCL_Filter.fasta -profile [docker/singularity/conda choose accordingly]

4. or run the example analysis without read filtering:

nextflow run pipesnake/ --input pipesnake/example/data/ToyData_SampleInfo.csv --outdir pipesnake/TEST2 --blat_db pipesnake/example/data/ToyData_SqCL_25Targets.fasta -profile [docker/singularity/conda choose accordingly]

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Monitoring Resource Usage

The included example dataset runs on a mid-tier local machine (88 CPU, 94 Gb memory) in <4 minutes.
Once your analysis is done, you can find information on resource usage in the tracing/pipeline_info/ directory of your output directory.

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