_viash.yaml

viash_version: 0.9.0

name: task_ist_preprocessing
organization: openproblems-bio
version: dev

license: MIT
keywords: [spatial transcriptomics, imaging-based spatial transcriptomics, preprocessing]
links:
  issue_tracker: https://github.com/openproblems-bio/task_ist_preprocessing/issues
  repository: https://github.com/openproblems-bio/task_ist_preprocessing
  docker_registry: ghcr.io

label: iST Preprocessing
summary: Benchmarking approaches for preprocessing imaging-based spatial transcriptomics

# TODO: Add a description.
description: |
  Provide a clear and concise description of your task, detailing the specific problem it aims
  to solve. Outline the input data types, the expected output, and any assumptions or constraints.
  Be sure to explain any terminology or concepts that are essential for understanding the task.

  Explain the motivation behind your proposed task. Describe the biological or computational 
  problem you aim to address and why it's important. Discuss the current state of research in
  this area and any gaps or challenges that your task could help address. This section 
  should convince readers of the significance and relevance of your task.

# references:
#   doi:
#     - 10.21203/rs.3.rs-4181617/v1
  
info:
  image: The name of the image file to use for the component on the website.
  test_resources:
    - type: s3
      path: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium_rep1/
      dest: resources_test/common/2023_10x_mouse_brain_xenium_rep1/
    - type: s3
      path: s3://openproblems-data/resources_test/common/2023_yao_mouse_brain_scrnaseq_10xv2/
      dest: resources_test/common/2023_yao_mouse_brain_scrnaseq_10xv2/
    - type: s3
      path: s3://openproblems-data/resources_test/task_ist_preprocessing/
      dest: resources_test/task_ist_preprocessing

authors: 
  - name: Louis Kümmerle
    roles: [ author, maintainer ]
    info: 
      github: LouisK92
      orcid: 0000-0002-9193-1243
  - name: Malte D. Luecken
    roles: [ author ]
    info:
      github: LuckyMD
      orcid: 0000-0001-7464-7921
  - name: Daniel Strobl
    roles: [ author ]
    info:
      github: danielStrobl
      orcid: 0000-0002-5516-7057
  - name: Robrecht Cannoodt
    roles: [ author ]
    info:
      github: rcannood
      orcid: "0000-0003-3641-729X"

config_mods: |
  .runners[.type == "nextflow"].config.labels := { lowmem : "memory = 20.Gb", midmem : "memory = 50.Gb", highmem : "memory = 100.Gb", lowcpu : "cpus = 5", midcpu : "cpus = 15", highcpu : "cpus = 30", lowtime : "time = 1.h", midtime : "time = 4.h", hightime : "time = 8.h", veryhightime : "time = 24.h" }

repositories:
  - name: openproblems
    type: github
    repo: openproblems-bio/openproblems
    tag: build/main
  - name: core
    type: github
    repo: openproblems-bio/core
    tag: build/main
    path: viash/core