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#
# 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: 'Beibei Chen'
# A contact email address for questions
email: 'biohpc-help@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 a simple ChIP-seq analysis workflow using deepTools, Diffbind, ChipSeeker and MEME-ChIP, 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', 'chipseq-analysis']
# -----------------------------------------------------------------------------
# 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:
- 'deeptools/2.3.5'
- 'meme/4.11.1-gcc-openmpi'
# 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: bams
type: files
required: true
description: |
Bam files of all samples
- id: peaks
type: files
required: true
description: |
Peak files of all samples. Peaks should be sorted by user using either p_value or intensity of the signals.Bed format.
- id: design
type: files
required: true
regex: ".*(csv)"
description: |
A design file listing pairs of sample name and sample group. Must be in csv format
Columns must include: SampleID,Tissue, Factor, Condition, Replicate, Peaks, bamReads, bamControl, ControlID, PeakCaller
- [ '/project/shared/bicf_workflow_ref/GRCh38', 'human GRCh38']
- [ '/project/shared/bicf_workflow_ref/GRCh37', 'human GRCh37']
- [ '/project/shared/bicf_workflow_ref/GRCm38', 'mouse GRCm38']
required: true
description: |
Reference genome for annotation
The number of top peaks to use for motif discovery. This program won't sort peak BED files for you, so please make sure your peak files are already sorted. Default : -1, use all the peaks
default: -1
# -----------------------------------------------------------------------------
# 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
vizapp_bioc_packages:
- qusage
# - ballgown
vizapp_github_packages:
- js229/Vennerable