- Remove debug logging and dead PVC/direct-path fallbacks from main.nf
- Remove nf-amazon plugin and PVC storage config from nextflow.config
(S3 access is handled by boto3 in the script)
- Simplify input download and output upload to single boto3 blocks
PVC mount is not available in k8s pods. Try multiple fallback
methods to retrieve input PDB: PVC path, s3-to-PVC conversion,
AWS CLI from MinIO, and curl from MinIO. Also add nf-amazon
plugin and s3:// default paths.
- Add executor, docker, k8s storage config to k8s profile
- Use val input instead of file channel (avoids S3 staging issue)
- Pass PDB path as string, copy from PVC mount inside script
- Add PVC mount debug logging
- Set default params to /omic/eureka paths
WES does not stage S3 input files to the Nextflow workdir.
Adding nf-amazon plugin so Channel.of(file(params.pdb)) can
resolve s3:// paths directly from MinIO without WES staging.
- Match p2rank's working config structure: k8s profile only sets container
- Let WES-generated profile.config handle executor, storage, and k8s settings
- Add memory (8GB) and cpu (2) resource requests
- Set params defaults to null (values provided by WES experiment_params)
- Add manifest metadata
