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HuBMAP scRNA-seq pipeline: Salmon, Scanpy, scVelo

Overview

The HuBMAP scRNA-seq pipeline is built on Salmon, Scanpy, and scVelo, and is implemented as a CWL workflow wrapping command-line tools encapsulated in Docker containers.

Requirements

Running the pipeline requires a CWL workflow execution engine and container runtime; we recommend Docker and the cwltool reference implementation. cwltool is written in Python and can be installed into a sufficiently recent Python environment with pip install cwltool. Afterward, clone this repository, check out a tag, and invoke the pipeline as:

cwltool pipeline.cwl --assay ASSAY --fastq_dir FASTQ_DIR --threads THREADS

At least 28GB memory is required for the Salmon quantification step; this memory usage is due to inclusion of the entire GRCh38 reference genome as decoy sequences in the quantification index. See https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02151-8 for more details.

(The master branch and latest published Docker images may not always be in sync; checking out a version like v2.0.6 is highly recommended before running the pipeline, unless building Docker images locally.)

Supported assays:

  • 10x_v2 (single-cell)
  • 10x_v2_sn (single-nucleus)
  • 10x_v3 (single-cell)
  • 10x_v3_sn (single-nucleus)
  • snareseq
  • sciseq
  • slideseq
  • multiome_10x