Package: capcruncher
CapCruncherThe CapCruncher package is designed to process Capture-C, Tri-C and Tiled-C data. Unlike other pipelines that are designed to process Hi-C or Capture-HiC data, the filtering steps in CapCruncher are specifically optimized for these datasets. The package consists of a configurable data processing pipeline and a supporting command line interface to enable fine-grained control over the analysis. The pipeline is fast, robust and scales from a single workstation to a large HPC cluster. It is designed to be run on an HPC cluster and can be configured to use a variety of package management systems, such as conda and singularity. For more information, see thedocumentation.Note:The current version of CapCruncher is in beta. Please report any issues you encounter to theissue trackerQuick StartInstallationWarning:CapCruncher is currently only availible for linux with MacOS support planned in the future.CapCruncher is available on conda and PyPI. To install the latest version, run:pipinstallcapcruncherormambainstall-cbiocondacapcruncherPlease note that it is highly recommended to install CapCruncher in a conda environment. If you do not have conda installed, please follow the instructionshereto install mambaforge.See theinstallation guidefor more detailed instructions.UsageCapCruncher commands are run using thecapcrunchercommand. To see a list of available commands, run:capcruncher--helpTo see a list of available options for a command, run:capcruncher<command>--helpSee theCLI Referencefor more detailed information regarding the various subcommands.PipelineThe CapCruncher pipeline handles the processing of raw data from the sequencer to the generation of a contact matrix, generation of plots and production of a UCSC genome browser track hub. See thepipeline guidefor more detailed instructions including how to configure the pipeline to run onHPC clustersand use various package management systemscondaandsingularity.Pipeline ConfigurationThe pipeline is configured using a YAML file but it is strongly recommended to use thecapcruncher pipeline-configcommand to generate a tailored config file. To use the command, run:capcruncherpipeline-configSimply follow the prompts to generate a config file. See thepipeline configuration guidefor more detailed instructions.Running the pipelineThe pipeline is run using thecapcruncher pipelinecommand. Ensure that you have a configuration file and the fastq files to process are in the current working directory.# Basic usagecapcruncherpipeline--cores<NUMBEROFCORESTOUSE># Real example running the pipeline with 8 cores, using the slurm profile for running on a cluster with a SLURM workflow management system and using singularity for dependency managementcapcruncherpipeline--cores8--profileslurm--use-singularityNote:In order to avoid disconnecting from the cluster, it is recommended to run the pipeline in atmuxsession. Alternatively,nohupcan be used to run the pipeline in the background. For example:# tmux exampletmuxnew-scapcruncher
capcruncherpipeline--cores8--profileslurm--use-singularity# nohup examplenohupcapcruncherpipeline--cores8--profileslurm--use-singularity&See thepipeline guidefor more detailed instructions.