# # 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: -