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feat(tiberius): add prediction, merge, and scatter workflow - #34
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Integrates Tiberius as Nextflow modules, a reusable subworkflow, and a standalone workflow. Scatter modes none/chromosome/weighted; merge restores FASTA order and rewrites gene IDs by (seqid, start, strand).
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Summary
Integrates Tiberius as Nextflow modules, a reusable subworkflow, and a standalone workflow.
TIBERIUS_PREDICT(process_high+process_gpu); scatter jobs emit GTF onlyTIBERIUS_MERGEwrapsmerge_annotations.py, restores FASTA record order, writes GTF/GFF3, and optionally extracts protein/CDS from the merged annotation plus the original genome(seqid, start, strand), not chunk orderFXSPLIT -Hheader mode for whole-record chromosome scatternone,chromosome(default),weighted(--tiberius_bins)Uses
ghcr.io/hillerlab/tiberius:latest. Depends on the containers PR that publishes that image.nextflow run hillerlab/core \ -entry TIBERIUS \ -c hillerlab.config \ --genome genome.fa \ --model_cfg mammalia_nosoftmasking_v2 \ --output_dir results \ --tiberius_scatter chromosome \ -profile slurm,apptainer,gpuTest plan
nextflowstub-run ofTIBERIUS_PREDICT+TIBERIUS_MERGE(docker.enabled=false)merge_annotations.py(colliding chunk IDs rewritten)ghcr.io/hillerlab/tiberiusonce the container PR is published-profile gpu)