Slurm workflow for assembly, repeat annotation, structural annotation, and functional annotation of an Akodon genome. This repository reorganizes previously separate HPC job scripts into one reproducible workflow.

Assembly:

1. Supernova
2. supernova mkoutput
3. scaffold filtering with seqkit
4. QUAST
5. BUSCO
6. BUSCO plot
7. MultiQC
8. RepeatModeler
9. repeat library merge and CD-HIT filtering
10. RepeatMasker

Annotation:

11. simplify masked genome headers
12. download reference proteins from NCBI
13. prepare combined protein FASTA
14. GALBA
15. BRAKER2
16. BRAKER3
17. TSEBRA
18. longest-isoform filtering
19. restore original headers
20. InterProScan

Notes:

• stages 14, 15, and 16 are alternative prediction tracks
• TSEBRA combines selected predictor outputs
• the annotation branch starts after RepeatMasker
• Supernova should use raw, untrimmed 10x linked-read FASTQs

• Supernova
• seqkit
• QUAST
• BUSCO
• MultiQC
• RepeatModeler / RepeatMasker via dfam/tetools
• GALBA
• BRAKER2 / BRAKER3
• TSEBRA
• InterProScan

• config/pipeline.env: pipeline paths and Slurm settings
• config/bootstrap.env: dependency bootstrap settings
• config/samples.tsv: sample metadata
• run_pipeline.sh: full workflow submission
• run_smoke_test.sh: smoke test
• slurm/: numbered stage scripts
• scripts/check_pipeline_connections.sh: preflight path check
• scripts/hpc/bootstrap_dependencies.sh: HPC bootstrap

• raw 10x FASTQs in data/
• sample table in config/samples.tsv
• BUSCO lineage data
• container images for RepeatModeler/RepeatMasker, BRAKER, GALBA, and InterProScan
• annotation inputs such as ncbi_dataset.tsv, protein FASTA, TSEBRA configs, and RNA BAMs for BRAKER3

Review:

• config/pipeline.env
• config/bootstrap.env

Common settings:

• DATA_DIR
• SUPERNOVA_BIN
• REPEATMODELER_IMAGE
• BUSCO_LINEAGE_DIR
• BRAKER_SIF
• GALBA_SIF
• INTERPROSCAN_SIF
• INTERPROSCAN_DATA_DIR
• Slurm account, partition, QoS, memory, and walltime

bash scripts/hpc/probe_node_capabilities.sh
bash scripts/hpc/bootstrap_dependencies.sh install config/bootstrap.env
bash scripts/hpc/bootstrap_dependencies.sh verify config/bootstrap.env

Automated by default:

• repo-local Conda environments
• BUSCO lineage download
• tetools_latest.sif
• InterProScan image and data
• get_longest_isoform.py
• default TSEBRA config files

Still manual by default:

• Supernova if the legacy path is unavailable
• BRAKER and GALBA SIFs unless source paths are provided
• biological inputs such as Vertebrata.fa, ncbi_dataset.tsv, and RNA BAMs

Preflight:

bash scripts/check_pipeline_connections.sh config/pipeline.env

Submit:

bash run_pipeline.sh config/pipeline.env

Smoke test:

bash run_smoke_test.sh config/smoke_test.env