FLASHApp/app.yaml at develop · OpenMS/FLASHApp · GitHub

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# App spec: what this app is. Schema and checker come from the template
# (utils/app_spec.schema.json, `python -m utils.app_spec`); the weekly
# template-sync job reads `template:` and `sync.app_owned` from here.
# App-owned: template syncs never overwrite this file.
spec_version: 1
template:
  repository: OpenMS/streamlit-template
  branch: main
app:
  slug: flashapp
  name: FLASHApp
  description: 'Top-down proteomics: FLASHDeconv deconvolution, FLASHTnT tag-based identification and
    FLASHQuant quantification, with a configurable linked viewer.'
  repository: OpenMS/FLASHApp
  domain: top-down-proteomics
  image: ghcr.io/openms/flashapp
inputs:
  mzML-files:
    types:
    - mzML
    - raw
    - d
    multiple: true
    description: Top-down LC-MS runs; .raw and .d are converted.
  fasta-file:
    types:
    - fasta
    - peff
    multiple: false
    description: Protein database for FLASHTnT.
workflows:
- name: FLASHDeconv
  class: src/Workflow.py:DeconvWorkflow
  inputs:
  - mzML-files
  steps:
  - tool: FLASHDeconv
    in: mzML-files
- name: FLASHTnT
  class: src/Workflow.py:TagWorkflow
  inputs:
  - mzML-files
  - fasta-file
  steps:
  - tool: DecoyDatabase
    in: fasta-file
  - tool: FLASHDeconv
    in: mzML-files
  - tool: FLASHTnT
    in: FLASHDeconv
  - tool: FLASHAnnotator
    optional: true
- name: FLASHQuant
  class: src/Workflow.py:QuantWorkflow
  steps: []
results:
- role: custom
  workflow: FLASHDeconv
  title: Viewer (Vue grid)
  page: content/FLASHDeconv/FLASHDeconvViewer.py
- role: custom
  workflow: FLASHTnT
  title: Viewer (Vue grid)
  page: content/FLASHTnT/FLASHTnTViewer.py
- role: custom
  workflow: FLASHQuant
  title: Viewer
  page: content/FLASHQuant/FLASHQuantViewer.py
pages:
- content/quickstart.py
- content/user_guide.py
- content/FLASHDeconv/FLASHDeconvWorkflow.py
- content/FLASHDeconv/FLASHDeconvSequenceInput.py
- content/FLASHDeconv/FLASHDeconvLayoutManager.py
- content/FLASHDeconv/FLASHDeconvViewer.py
- content/FLASHDeconv/FLASHDeconvDownload.py
- content/FLASHTnT/FLASHTnTWorkflow.py
- content/FLASHTnT/FLASHTnTLayoutManager.py
- content/FLASHTnT/FLASHTnTViewer.py
- content/FLASHTnT/FLASHTnTDownload.py
- content/FLASHQuant/FLASHQuantFileUpload.py
- content/FLASHQuant/FLASHQuantViewer.py
deploy:
  k8s:
    enabled: true
    hosts:
    - flashapp.webapps.openms.de
    - flashapp.webapps.openms.org
    worker_tier: high
  docker_compose: true
  desktop:
  - windows
  online_deployment: false
sync:
  app_owned:
  - app.yaml
  - app.py
  - settings.json
  - default-parameters.json
  - presets.json
  - README.md
  - content/*
  - src/python-tools/*
  - example-data/*
  - assets/*
  - k8s/*
  - .github/workflows/build-and-test.yml
  - .github/kind-config.yaml
  - CLAUDE.md
  - src/Workflow.py
  - js-component/*
  - .gitmodules
  - openms-streamlit-vue-component
  - src/parse/*
  - src/render/*
  - tests/test_tasks.py
  - tests/test_workspace_sync.py
  - tests/test_seed_demos.py
  - tests/test_run_manager.py