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.
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
(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)snareseqsciseqslideseq