changes made from origin/samh/amr-dev to run on vwb

[v-dlay]

DO NOT MERGE: SHOWING DIFF CHANGES FOR RUNNING ON VWB UI

Within UI:
nextflow run main_AMR++.nf
-profile workbench
-params-file params_google_batch.yaml

New files
- params_google_batch.yaml — YAML version of the GCP params (required because -params-file only accepts JSON/YAML)
- scripts/config/wb.env — env var file with all Workbench values hardcoded

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Modified files

nextflow.config — hardcoded all workbench profile values (previously used env vars):
- Container image: us-central1-docker.pkg.dev/vwb-dev-beaming-sprout-9366/nf-containers/amrplusplus-workbench:latest
- workDir, google.project, google.region, network, subnetwork, service account email

params_google_batch.config — replaced dynamic ${gcs_bucket} env var with hardcoded GCS paths:
- All data paths → gs://sam-nextflow-vwb-dev-beaming-sprout-9366/amr-on-wb/data/...
- Output → gs://sam-nextflow-vwb-dev-beaming-sprout-9366/amr-on-wb/results/test_results
- Added pipeline = "fast_AMR" so it doesn't need to be passed on CLI
- Changed snp = "N" — AmrPlusPlus_SNP binary not present in bin/, would cause failure

modules/Microbiome/kraken2.nf — removed kronadb and kronafromkraken processes (dead DSL1 code causing Cannot invoke method optional() crash at parse time)

scripts/upload_data.sh — fixed destination path to include amr-on-wb/ prefix so data lands at the correct GCS location