#
# 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?
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: '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
test the astrocyte platform. Please note that start from publish version
0.0.8 and test version 0.0.2, this workflow will only support Astrocyte 0.4.0
and above.
#### 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.
# 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: '0.4.0'
# 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: '20.01.0'
# (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: 'singularity'
# 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', '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
# 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: story
type: files
required: true
description: |
A text file containing a story
regex: ".*(txt)"
min: 1
- 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
- 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' ]
# -----------------------------------------------------------------------------
# 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:
-