Quickstart

Use this section to test the runability of the pipeline

A more comprehensive step-by-step-guide for the setup of the pipeline and the test on real data can be found in the Installation section.

Requirements

See Requirements. Make sure to have Nextflow and Singularity or Docker installed

Test the runability of the quicksand pipeline using the included test-data:

nextflow run mpieva/quicksand -profile singularity,test

See the final_report.tsv for a summary of the results.

See the Output section for a detailed explaination of all the output files.

heap-space error: Nextflow related error, not enough memory allocated for the Java Virtual machine to run the processes. Manually set the memory for nextflow by typing export NXF_OPTS="-Xms128g -Xmx128g" before the run
file-not found error: Your Singularity installation might not allow auto-mounting of paths: See Singularity