hisplan/cromsfer

Cromwell Output Transfer

Cromwell Output Transfer (Cromsfer)

Transfers output files from Cromwell/WDL workflows to a designated S3 locations with a human-friendly directory structure. It supports:

• FastQC (FASTQ QC)
• Sharp (Hashtag and CellPlex)
• Sharp (CITE-seq)
• Sharp (ASAP-seq)
• Velopipe (RNA Velocity)
• Cell Ranger V(D)J
• Cell Ranger GEX
• Cell Ranger ATAC
• Cell Ranger ARC
• Cell Ranger CellPlex
• Space Ranger
• Transgenes for Cell Ranger
• Transgenes for SEQC
• ArchR Stand Alone (aka. ArchRSA)
• ArchR + Cell Ranger (aka. ArchRCR)
• mkref (Generating genome index for STAR aligner)
• Mito Tracing

Prerequisites

• AWS CLI (for Amazon Web Services)
• gsutil (for Google Cloud Platform)

Development Environment

Install Cromsfer

conda create -n cromsfer python=3.8 pip
conda activate cromsfer
git clone https://github.com/hisplan/cromsfer.git
pip install -e .[dev]

Run Redis

docker run --rm -d -p 6379:6379 redis:5.0.6

Run the Poller Service

cromsfer.poller picks up the workflows that have been completed, but not yet transferred.

cromsfer.poller --config config.dev.aws.us-east-1.yaml

Run the Transfer Service

cromsfer.transfer transfers the output files to the final destination.

cromsfer.transfer  --config config.dev.aws.us-east-1.yaml

Utilities

Getting the metadata for a given workflow:

$ cd utils
$ ./get-metadata.sh \
    -c ../config.aws.us-east-1.yaml \
    -w 4bb895a2-dc44-4d6d-94ca-1294452e1bf8

Resetting the transfer status (i.e. "-")

$ cd utils
$ ./transfer-reset.sh \
    -c ../config.aws.us-east-1.yaml \
    -w 4bb895a2-dc44-4d6d-94ca-1294452e1bf8

Deployment

1. Make sure you increment the version number (src/cromsfer/version.py).
2. Push all the changes into the GitHub repository.
3. Create a release tag in the GitHub repository.
4. Build a docker image.