A Nextflow pipeline based on GeoDock.
Follow this to install Nextflow: https://www.nextflow.io/docs/latest/getstarted.html
nextflow pull juyeongkim/geodockDownloaded pipeline are stored in the folder $HOME/.nextflow/assets.
--partner1 |
--partner2 |
--output |
|---|---|---|
| 1.pdb | x.pdb | 1._.x.pdb |
| 2.pdb | y.pdb | 1._.y.pdb |
| 3.pdb | 2._.x.pdb | |
| 4.pdb | 2._.y.pdb | |
| 3._.x.pdb | ||
| 3._.y.pdb | ||
| 4._.x.pdb | ||
| 4._.y.pdb |
cd /where/you/want/to/store/logs/and/intermediate/files
nextflow pull juyeongkim/geodock
nextflow run juyeongkim/geodock -r main --partner1 /your/partner1/dir --partner2 /your/partner2/dir --output /your/output/dirAlternatively, you can run the pipeline on HPC with slurm. First, load the environment modules if they are available. If not, please follow the Apptainer and Nextflow documentation to install them first.
module load Apptainer
module load Nextflow
cd /where/you/want/to/store/logs/and/intermediate/files
nextflow pull juyeongkim/geodock
nextflow run juyeongkim/geodock -r main -profile cluster --partner1 /your/partner1/dir --partner2 /your/partner2/dir --output /your/output/dir
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