# # metadata for the example astrocyte ChipSeq workflow package # # ----------------------------------------------------------------------------- # BASIC INFORMATION # ----------------------------------------------------------------------------- # A unique identifier for the workflow package, text/underscores only name: 'chipseq_analysis_bicf' # Who wrote this? author: 'Holly Ruess, Spencer D. Barnes, Beibei Chen and Venkat Malladi' # A contact email address for questions email: 'bicf@utsouthwestern.edu' # A more informative title for the workflow package title: 'BICF ChIP-seq Analysis Workflow' # A summary of the workflow package in plain text description: | This is a workflow package for the BioHPC/BICF ChIP-seq workflow system. It implements ChIP-seq analysis workflow and visualization 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: - 'index.md' # ----------------------------------------------------------------------------- # 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' - 'trimgalore/0.4.1' - 'bwa/intel/0.7.12' - 'samtools/1.6' - 'sambamba/0.6.6' - 'bedtools/2.26.0' - 'deeptools/2.5.0.1' - 'phantompeakqualtools/1.2' - 'macs/2.1.0-20151222' - 'UCSC_userApps/v317' - 'R/3.3.2-gccmkl' - 'meme/4.11.1-gcc-openmpi' - 'pandoc/2.7' # 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: reads type: files required: true description: | One or more input FASTQ files from a ChIP-seq expereiment and a design file with the link bewetwen the same file name and sample id regex: ".*(fastq|fq)*gz" min: 2 - id: pairedEnd type: select required: true choices: - [ 'true', 'true'] - [ 'false', 'false'] description: | If Paired-end: True, if Single-end: False. - id: designFile type: file required: true description: | A design file listing sample id, fastq files, corresponding control id and additional information about the sample. regex: ".*txt" - id: genome type: select required: true choices: - [ 'GRCh38', 'Human GRCh38'] - [ 'GRCh37', 'Human GRCh37'] - [ 'GRCm38', 'Mouse GRCm38'] description: | Reference species and genome used for alignment and subsequent analysis. - id: skipDiff type: select required: true choices: - [ 'true', 'true'] - [ 'false', 'false'] description: | Skip differential peak analysis - id: skipMotif type: select required: true choices: - [ 'true', 'true'] - [ 'false', 'false'] description: | Skip motif calling - id: skipPlotProfile type: select required: true choices: - [ 'true', 'true'] - [ 'false', 'false'] description: | Skip Plot Profile Analysis - id: astrocyte type: select choices: - [ 'true', 'true' ] required: true default: 'true' description: | Ensure configuraton for astrocyte. # ----------------------------------------------------------------------------- # 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: []