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#
# metadata for the example astrocyte ChipSeq workflow package
#

# -----------------------------------------------------------------------------
# BASIC INFORMATION
# -----------------------------------------------------------------------------

# A unique identifier for the workflow package, text/underscores only
name: 'example_wordcount'
# Who wrote this?
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author: 'David Trudgian, Peng Lian, Devin OKelly'
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# A contact email address for questions
email: 'biohpc-help@utsouthwestern.edu'
# A more informative title for the workflow package
title: 'Example Wordcount Workflow'
# A summary of the workflow package in plain text
description: |
  This is a minimal test workflow package that counts the occurences of words
  in a test file. It can be used as a template to develop workflows, and as to
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  test the astrocyte platform. Please note that start from publish version 
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  0.0.8 and test version 0.0.2, this workflow will only support Astrocyte 0.4.1
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  and above.
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#### New Features in Astrocyte 0.4.0 and above ####
citation: |
  Please cite individual programs and versions of pipeline
  used, and the overall pipeline doi: 12.3456/zenodo.9876543.
  Please cite in publications:
  Pipeline was developed by BioHPC.
  
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# The minimum Astrocyte version that requires to run this workflow. For old pipelines, which do not have this label 
# a default value of 0.3.1 will be assigned automatically. A request of minimum version less than 0.4.0 will be ignored.
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minimum_astrocyte_version: '0.4.1'
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# The Nextflow version that requires to run this workflow.  For old pipelines, which do not have this label 
# a default value of 0.31.0 will be assigned automatically. Please make sure the requested nextflow version is available
# in the module list.
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nextflow_version: '21.04.1'
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# (Optional) The Nextflow config file to use for this workflow. If provided, the file should exist in workflow/configs
nextflow_config: 'biohpc.config'
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# The container to use for this workflow, none/singularity. If omitted, the default value 'none' will be used.
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container: 'singularity'
# The version of singularity to use. This is required if container == 'singularity'
singularity_version: '3.5.3'

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# -----------------------------------------------------------------------------
# DOCUMENTATION
# -----------------------------------------------------------------------------

# A list of documentation file in .md format that should be viewable from the
# web interface. These files are in the 'docs' subdirectory. The first file
# listed will be used as a documentation index and is index.md by convention
# To supply a title for documentation use a pair of [ 'filename', 'title' ]

documentation_files:
  - [ 'index.md', 'Wordcount Help' ]

# -----------------------------------------------------------------------------
# NEXTFLOW WORKFLOW CONFIGURATION
# -----------------------------------------------------------------------------

# Remember - The workflow file is always named 'workflow/main.f'
#            The workflow must publish all final output into $baseDir

# A list of clueter environment modules that this workflow requires to run.
# Specify versioned module names to ensure reproducability.
workflow_modules:
  - Test
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# A list of container images requires to run this workflow.
# Specify full path and version names to ensure reproducability.
# This keyword is required when 'container' is specified in Astrocyte 0.4.1 and above
workflow_containers:
  - docker://ubuntu:latest
  - docker://centos:centos8
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# A list of parameters used by the workflow, defining how to present them,
# options etc in the web interface. For each parameter:
#
# REQUIRED INFORMATION
#  id:         The name of the parameter in the NEXTFLOW workflow
#  type:       The type of the parameter, one of:
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#                string      - A free-format string
#                integer     - An integer
#                real        - A real number
#                file        - A single file from user data
#                files       - One or more files from user data
#                select      - A selection from a list of values
#                multiselect - One or more selections from a list of values
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#  required:    true/false, must the parameter be entered/chosen?
#  description: A user friendly description of the meaning of the parameter
#
# OPTIONAL INFORMATION
#  default:   A default value for the parameter (optional)
#  min:       Minium value/characters/files for number/string/files types
#  max:       Maxumum value/characters/files for number/string/files types
#  regex:     A regular expression that describes valid entries / filenames
#
# SELECT TYPE
#  choices:   A set of choices presented to the user for the parameter.
#             Each choice is a pair of value and description, e.g.
# 
#             choices:
#               - [ 'myval', 'The first option']
#               - [ 'myval', 'The second option']
#
# NOTE - All parameters are passed to NEXTFLOW as strings... but they
#        are validated by astrocyte using the information provided above

workflow_parameters:

  - id: story
    type: files
    required: true
    description: |
      A text file containing a story
    regex: ".*(txt)"
    min: 1

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  - id: test_int
    type: integer
    required: true
    default: 123
    min: 1
    max: 1000
    description: |
      This is an example integer field, it is not used by the workflow

  - id: test_real
    type: real
    required: true
    default: 123.456
    min: 1
    max: 1000
    description: |
      This is an example real field, it is not used by the workflow
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  - id: test_string
    type: string
    required: true
    default: "Example"
    description: |
      This is an example string field, it is not used by the workflow

  - id: test_select
    type: select
    required: true
    default: "Dog"
    description: |
      This is an example select field, it is not used by the workflow
    choices:
      - [ 'Cat', 'Cat, Kitten' ]
      - [ 'Dog', 'Dog, Puppy' ]
      - [ 'Horse', 'Horse, Foal' ]

  - id: test_multiselect
    type: multiselect
    required: true
    default: "Banana"
    description: |
      This is an example multiselect field, it is not used by the workflow
    choices:
      - [ 'Apple', 'Green Apple' ]
      - [ 'Banana', 'Yellow Banana' ]
      - [ 'Strawberry', 'Red Strawberry' ]
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# -----------------------------------------------------------------------------
# SHINY APP CONFIGURATION
# -----------------------------------------------------------------------------

# Remember - The vizapp is always 'vizapp/server.R' 'vizapp/ui.R'
#            The workflow must publish all final output into $baseDir

# Name of the R module that the vizapp will run against
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vizapp_r_module: 'R/3.6.1-gccmkl'
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# List of any CRAN packages, not provided by the modules, that must be made
# available to the vizapp
vizapp_cran_packages:
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  - shiny
  - shinyFiles
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  - plotly 
    
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# # List of any Bioconductor packages, not provided by the modules, that must be made
# available to the vizapp
vizapp_bioc_packages:
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  -

# # List of any packages to install from GitHub using devtools, that must be
# made availavle to the vizapp
vizapp_github_packages:
  -