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#
# metadata for the  Astrocyte CellRanger mkfastq workflow package
#

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

# A unique identifier for the workflow package, text/underscores only
name: 'cellranger_mkfastq'
# Who wrote this?
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author: 'Gervaise H. Henr, Jon Gesell, Jeremy Mathews, and Venkat Malladi'
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# A contact email address for questions
email: 'bicf@utsouthwestern.edu'
# A more informative title for the workflow package
title: 'BICF CellRanger mkfastq Workflow'
# A summary of the workflow package in plain text
description: |
  This is a workflow package for the BICF/Strand Lab CellRanger mkfastq workflow system.
  It implements 10x CellRanger mkfastq analysis workflow application.

# -----------------------------------------------------------------------------
# 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
documentation_files:
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  - 'index.md'
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# -----------------------------------------------------------------------------
# NEXTFLOW WORKFLOW CONFIGURATION
# -----------------------------------------------------------------------------

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

# A list of cluster environment modules that this workflow requires to run.
# Specify versioned module names to ensure reproducability.
workflow_modules:
  - 'python/3.6.1-2-anaconda'
  - 'cellranger/2.1.1'
  - 'bcl2fastq/2.17.1.14'
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  - 'fastqc/0.11.5'
  - 'parallel'
  - 'multiqc/1.7'
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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:
#                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
#  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: bcl
    type: files
    required: true
    description: |
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      One or more input tarball (+/- gunzip) basecall files (bcl) from a sequencing of 10x single-cell expereiment (can be .tar or .tar.gz).
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    regex: ".*\\.tar*"
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    min: 1
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  - id: designFile
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    type: file
    required: true
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    regex: ".*\\.csv"
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    description: |
      A design file listing lane, sample, corresponding index.


# -----------------------------------------------------------------------------
# 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/3.2.1-intel'

# 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
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vizapp_bioc_packages: []