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astrocyte_pkg.yml
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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: 'Holly Ruess, Spencer D. Barnes, Beibei Chen and Venkat Malladi'
# A contact email address for questions
email: '[email protected]'
# 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: []