#
# 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: '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: |
Fully containerized, runs with Astrocyte/2.0.0, BioHPC registry, and SLURM.
#### 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: '2.0.0'
# 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: '22.04.5'
# (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: '3.9.9'
# -----------------------------------------------------------------------------
# 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 cluster environment modules that this workflow requires to run.
# Specify versioned module names to ensure reproducibility.
workflow_modules:
- Test
# A list of container images requires to run this workflow.
# Specify full path and version names to ensure reproducibility.
# This keyword is required when 'container' is specified in Astrocyte 0.4.1 and above.
# Singularity supports different registries, please specify the protocol to use.
# Such as, "docker://", "shub://", "library://", etc. We encourage you to use the GitLab
# container registry of BioHPC to save and manage your container images.
workflow_containers:
- docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/biohpc/astrocyte_example_wordcount/ubuntu:latest
- docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/biohpc/astrocyte_example_wordcount/centos:centos8
# 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: Maximum 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
# A containerized version is recommended.
vizapp_r_module: 'R/4.2.2-img'
# List of any CRAN packages, not provided by the modules, that must be made
# available to the vizapp
vizapp_cran_packages:
- shiny
- shinyFiles
- plotly
# # 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 available to the vizapp
vizapp_github_packages:
-