Tags

fix(alphafold3): retry every process per task and skip only the failed task

- Set errorStrategy to retry up to 5 times per task, then ignore, as the
  default for all processes. Previously only alphafold3 and inference_stage
  retried, so one failed parameters/msa_stage/cif_to_pdb task (e.g. module
  load failing on a node at job start) terminated the whole run and killed
  all other running tasks.
- Merge duplicated beforeScript/afterScript/resource settings for
  alphafold3 and inference_stage into one shared withName block.
- Merge parameters and cif_to_pdb resource settings.
- No change to queues, time limits, memory, cpus, or script contents.

Note: ignore skips a failed task silently; check trace.txt for FAILED rows
after each run.

Fixing Ticket#2026081710000342 — Astrocyte/AlphaFold3 screen:
1. Workflow cannot read multiple JSON files at the same time
2. Upstream file dependency issue to downstream process

fix: route large MSA to 512GB partition, increase memory to 480GB
Ticket#2026081710000342

DMZ does not contain H100 H200 partions, removed.

Refactor workflow: split MSA/inference stages, add dynamic routing by sequence length, add H200 partition support

The workflow `workflow/main.nf` has four processes:

- **parameters**: Parse the input JSON and count total residues
- **alphafold3** / **msa_stage + inference_stage**: Run structure prediction (see below)
- **cif_to_pdb**: Convert AlphaFold3 output from .cif to .pdb for downstream visualization

uncontainerized version of alphafold3/3.0.1

containerized version with module load alphafold3/3.0.1

fix bash file in cif_to_pdb

After migrating from rhel7 to rhel9.4, inside of the process cif_to_pdb, pymol/2.5 is renamed as py-pymol/2.5.0 on rhel9.

Fixed error: cannot run multiple files simultaneously
Vizapp containerized + cif2pdb

test passing multiple files

Fixed error: cannot run multiple files simultaneously
Vizapp containerized + cif2pdb

Vizapp containerized + cif2pdb

The vizapp part is containerized

make cif_to_pdb into folder channel instead of files channel

This version removes cif_to_pdb process, makes vizapp available to read in cif files.

remove cif2pbd

vizapp