Connectoflow pipeline

=======================

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 Apptainer (Singularity), launch your Nextflow command with: -with-singularity ABSOLUTE_PATH/scilus-2.2.3.sif

⚠️ Singularity image and docker are not available yet.

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:2.2.3

⚠️ WARNING ⚠️

The official release 2.2.3 is NOT available now.

Please, either build the singularity container using this command:

singularity build scilus_dev.sif docker://scilus/scilus:dev

and then launch your Nextflow command with: -with-singularity ABSOLUTE_PATH/scilus_latest.sif

Or launch your Nextflow command with docker: -with-docker scilus/scilus:dev

Usage

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