#
# metadata for the example astrocyte ChipSeq workflow package
#

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

# A unique identifier for the workflow package, text/underscores only
name: 'astrocyte_example'
# Who wrote this?
author: 'David Trudgian, Peng Lian'
# A contact email address for questions
email: 'biohpc-help@utsouthwestern.edu'
# A more informative title for the workflow package
title: 'Astrocyte Example ChIPSeq Workflow'
# A summary of the workflow package in plain text
description: |
  This is an example workflow package for the BioHPC astrocyte workflow system.
  It implements a simple ChIPSeq analysis workflow using BWA and MACS, plus a
  simple R Shiny visualization application. Please note that start from publish 
  version 0.0.8 and test version 0.0.1, this workflow will only support 
  Astrocyte 0.4.1 and above.

# 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.
minimum_astrocyte_version: '0.4.1'
# 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.
nextflow_version: '21.04.1'
# (Optional) The Nextflow config file to use for this workflow. If provided, the file should exist in workflow/configs
nextflow_config: 'biohpc.config'
# The container to use for this workflow, none/singularity. If omitted, the default value 'none' will be used.
container: 'none'
# The version of singularity to use. This is required if container == 'singularity'
singularity_version: '3.5.3'

# -----------------------------------------------------------------------------
# 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', 'ChIPSeq Example' ]

# -----------------------------------------------------------------------------
# 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:
  - 'BWA/0.7.5'
  - 'picard/1.127'
  - 'macs/1.4.2'

# 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:
#  -

# 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:
#                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
#
#  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: fastq
    type: files
    required: true
    description: |
      One or more input FASTQ files from a ChIPSeq experiment
    regex: ".*(fastq|fq)"
    min: 1

  - id: index
    type: select
    choices:
      - [ '/project/apps_database/iGenomes/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/genome.fa', 'UCSC hg38']
      - [ '/project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa', 'UCSC hg19']
      - [ '/project/apps_database/iGenomes/Homo_sapiens/UCSC/hg18/Sequence/BWAIndex/genome.fa', 'UCSC hg18']
      - [ '/project/apps_database/iGenomes/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/genome.fa', 'UCSC mm10']
      - [ '/project/apps_database/iGenomes/Mus_musculus/UCSC/mm9/Sequence/BWAIndex/genome.fa', 'UCSC mm9']
    required: true
    description: |
      Reference genome for BWA alignment

# -----------------------------------------------------------------------------
# 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
vizapp_r_module: 'R/3.4.1-gccmkl'

# List of any CRAN packages, not provided by the modules, that must be made
# available to the vizapp
vizapp_cran_packages:
  - shiny
  - shinyFiles

# List of any Bioconductor packages, not provided by the modules, that must be made
# available to the vizapp
vizapp_bioc_packages:
  -

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