czb-util

A collection of scripts for common data management and processing tasks.

The provided pipelines are built using the Viash framework on top of the Nextflow workflow system. For more information on Nextflow please visit the Nextflow github page and the Nextflow read the docs page.

Requirements

Install Docker, Podman or Singularity.
Install Nextflow.

Run versioned pipeline

These are instructions on how to launch a pipeline using the published code without cloning and using this repository.

Running Cell Ranger Demux

nextflow \
  run https://github.com/czbiohub/utilities \
  -r 1.0.0 \
  -main-script workflows/1_ingestion/cellranger_demux/main.nf \
  -resume \
  -latest \
  -with-docker \
  --id tiny_bcl \
  --input resources_test/cellranger_tiny_bcl/bcl \
  --sample_sheet resources_test/cellranger_tiny_bcl/bcl/sample_sheet.csv \
  --publishDir temp

Running Cell Ranger Mapping

nextflow \
  run https://github.com/czbiohub/utilities \
  -r 1.0.0 \
  -main-script workflows/1_ingestion/cellranger_mapping/main.nf \
  -resume \
  -latest \
  -with-docker \
  --id tiny_fastq \
  --input resources_test/cellranger_tiny_fastq/cellranger_tiny_fastq \
  --reference resources_test/cellranger_tiny_fastq/cellranger_tiny_ref \
  --publishDir temp

Setting up development environment

Install Viash and Nextflow.

Run viash ns build --parallel --setup cb to build all components and Docker containers locally.

Run viash ns test --parallel to unit test all components.