fix PREP_SUBMISSION and UPDATE_SUBMISSION to stage batch_tsv and sample files as process inputs

[smanda4]

Description

Please Describe the Bug(s) Fixed and/or the Feature(s) Added:

Fixes FileNotFoundError failures in PREP_SUBMISSION and UPDATE_SUBMISSION on cloud executors (confirmed on Google Batch; applies to any executor with a URI-shaped workDir).

Root cause

PREP_SUBMISSION and UPDATE_SUBMISSION reference file paths through a val-typed meta/samples map (${meta.batch_tsv}, ${sample.fasta}, etc.). Because those are val inputs and not path inputs, Nextflow doesn't stage the referenced files into the task container. On cloud executors the paths resolve to raw workDir URIs (/tostadas-work/<hash>/...) that don't exist inside the container, and both modules fail before the submission scripts ever run.

Example failure on a cloud executor:

submission_prep.py --metadata_file /tostadas-work/<task-hash>/genbank/batch_1.tsv ...
FileNotFoundError: '/tostadas-work/<task-hash>/genbank/batch_1.tsv'

(where /tostadas-work/ is the workDir set in nextflow.config for the cloud executor)

Fix

Lift each per-sample file type out of the meta/samples map into an explicit path input list. Nextflow then stages each list into a per-type subdirectory in the work dir, and the script walks samples in the same order the upstream workflow emitted them, popping the next entry from each file iterator whenever the sample declares that key. Same pattern used in 915d2b3 for submission_config staging in METADATA_VALIDATION.

Files touched:

• modules/local/prep_submission/main.nf — tuple input now includes staged batch_tsv plus five path lists (fastas, gffs, fq1s, fq2s, nnps); script uses iterators to zip samples with staged files
• modules/local/update_submission/main.nf — tuple input includes staged batch_tsv; script references $batch_tsv
• subworkflows/local/submission.nf — updated take comment
• workflows/genbank.nf — submission_batch_ch now emits a 9-item tuple
• workflows/biosample_and_sra.nf — same shape (fq1/fq2/nnp populated instead of fasta/gff)
• workflows/biosample_update.nf — rebatch_ch tuple includes tsv_file

Drive-by fix

While in PREP_SUBMISSION I noticed the sample_args builder was checking sample.get("nnp") but referencing sample.nanopore. Upstream workflows populate the "nanopore" key, so the "nnp" check was always false and nanopore samples were silently omitted from sample_args. Fixed to check the correct "nanopore" key.

Checklist

Go Through Checklist Below and Place A ✔️ (X Inside the Box) if Completed

General Checks

• Have you run appropriate tests (unit/integration/end-to-end) to check logic across run environments (Conda/Docker/Singularity on Scicomp/AWS/NF Tower/Local)?

  Validated end-to-end on Docker + Google Batch for the genbank workflow:

  • Dry-run on single-sample test data (AF266288, a public GenBank accession) completed cleanly
  • Output artifacts confirmed: .sqn, .tbl, .zip, VADR reports
  • prep_submission.log shows table2asn ran, biomol updated to cRNA, pub block stripped
  • Generated .sqn opens with a proper Seq-submit ::= { ASN.1 header and populated contact/affiliation blocks

  Did not test Conda / Singularity / Scicomp / AWS / NF Tower / Local execution paths, nor the biosample_and_sra or biosample_update workflows (no biosample test data available in the environment). Those workflows use the same channel-wiring pattern as genbank and the fix was applied identically, so they should work, but happy to gate on additional testing if the reviewer wants.

• Have you conducted proper linting procedures?

  • Block comments added at each change explaining the WHY (why files need to be lifted out of val, why iterator coercion is needed)
  • Variable naming matches existing tostadas conventions
  • Numpy docstrings / class-formatting rules don't apply (Nextflow / Groovy, no Python touched)

• Have you updated existing documentation (README.md, etc.) or created new ones within docs?

  Bug fix, not a new feature. Existing README doesn't need changes. Happy to add a "cloud executor support" note if the reviewer prefers.

CDC Checks

• Did you check for sensitive data, and remove any?

  Confirmed: no infrastructure identifiers, credentials, or environment-specific paths in the diff or PR body. Comments use generic examples.

• If you added or modified HTML, did you check that it was 508 compliant?

  N/A — no HTML in this PR.

Are additional approvals needed for this change? If so, please mention them below:

Not that I'm aware of, but please flag if there are.

Are there potential vulnerabilities or licensing issues with any new dependencies introduced? If so, please mention them below:

No new dependencies introduced.