arnaudbore / connectoflow

Connectoflow pipeline

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Run our state-of-the-art connectivity pipeline

If you use this pipeline, please cite:

Kurtzer GM, Sochat V, Bauer MW Singularity: Scientific containers for
mobility of compute. PLoS ONE 12(5): e0177459 (2017)
https://doi.org/10.1371/journal.pone.0177459

P. Di Tommaso, et al. Nextflow enables reproducible computational workflows.
Nature Biotechnology 35, 316–319 (2017) https://doi.org/10.1038/nbt.3820

Requirements

• Nextflow
• scilpy

Singularity/Docker

If you are on Linux, we recommend using the Singularity to run connectoflow pipeline. If you have Singularity == 3.*, launch your Nextflow command with: -with-singularity scilus/scilus:1.2.1_connectoflow-1.1.0

If you have rebuild singularity Singularity == 2.* image is available here Launch your Nextflow command with: -with-singularity ABSOLUTE_PATH/scilus-1.2.1_connectoflow-1.1.0.img

If you are on MacOS or Windows, we recommend using the Docker container to run connectoflow pipeline. Launch your Nextflow command with: -with-docker scilus/scilus:1.2.1_connectoflow-1.1.0

Usage

See USAGE or run nextflow run main.nf --help