Commit e30cbd75 authored by David Trudgian's avatar David Trudgian
Browse files

dos2unix yaml to fix lint error

parent 08d97f26
#
# metadata for the example astrocyte ChipSeq workflow package
#
# -----------------------------------------------------------------------------
# BASIC INFORMATION
# -----------------------------------------------------------------------------
# A unique identifier for the workflow package, text/underscores only
name: 'astrocyte_example'
# Who wrote this?
author: 'David Trudgian'
# A contact email address for questions
email: 'biohpc-help@utsouthwestern.edu'
# A more informative title for the workflow package
title: 'Astrocyte Example ChIPSeq Workflow'
# A summary of the workflow package in plain text
description: |
This is an example workflow package for the BioHPC astrocyte workflow system.
It implements a simple ChIPSeq analysis workflow using BWA and MACS, plus a
simple R Shiny 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
# To supply a title for documentation use a pair of [ 'filename', 'title' ]
documentation_files:
- [ 'index.md', 'ChIPSeq Example' ]
# -----------------------------------------------------------------------------
# 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:
- 'BWA/0.7.5'
- 'picard/1.127'
- 'macs/1.4.2'
# 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: fastq
type: files
required: true
description: |
One or more input FASTQ files from a ChIPSeq experiment
regex: ".*(fastq|fq)"
min: 1
- id: index
type: select
choices:
- [ '/project/apps_database/iGenomes/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/genome.fa', 'UCSC hg38']
- [ '/project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa', 'UCSC hg19']
- [ '/project/apps_database/iGenomes/Homo_sapiens/UCSC/hg18/Sequence/BWAIndex/genome.fa', 'UCSC hg18']
- [ '/project/apps_database/iGenomes/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/genome.fa', 'UCSC mm10']
- [ '/project/apps_database/iGenomes/Mus_musculus/UCSC/mm9/Sequence/BWAIndex/genome.fa', 'UCSC mm9']
required: true
description: |
Reference genome for BWA alignment
# -----------------------------------------------------------------------------
# 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:
#
# metadata for the example astrocyte ChipSeq workflow package
#
# -----------------------------------------------------------------------------
# BASIC INFORMATION
# -----------------------------------------------------------------------------
# A unique identifier for the workflow package, text/underscores only
name: 'astrocyte_example'
# Who wrote this?
author: 'David Trudgian'
# A contact email address for questions
email: 'biohpc-help@utsouthwestern.edu'
# A more informative title for the workflow package
title: 'Astrocyte Example ChIPSeq Workflow'
# A summary of the workflow package in plain text
description: |
This is an example workflow package for the BioHPC astrocyte workflow system.
It implements a simple ChIPSeq analysis workflow using BWA and MACS, plus a
simple R Shiny 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
# To supply a title for documentation use a pair of [ 'filename', 'title' ]
documentation_files:
- [ 'index.md', 'ChIPSeq Example' ]
# -----------------------------------------------------------------------------
# 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:
- 'BWA/0.7.5'
- 'picard/1.127'
- 'macs/1.4.2'
# 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: fastq
type: files
required: true
description: |
One or more input FASTQ files from a ChIPSeq experiment
regex: ".*(fastq|fq)"
min: 1
- id: index
type: select
choices:
- [ '/project/apps_database/iGenomes/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/genome.fa', 'UCSC hg38']
- [ '/project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa', 'UCSC hg19']
- [ '/project/apps_database/iGenomes/Homo_sapiens/UCSC/hg18/Sequence/BWAIndex/genome.fa', 'UCSC hg18']
- [ '/project/apps_database/iGenomes/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/genome.fa', 'UCSC mm10']
- [ '/project/apps_database/iGenomes/Mus_musculus/UCSC/mm9/Sequence/BWAIndex/genome.fa', 'UCSC mm9']
required: true
description: |
Reference genome for BWA alignment
# -----------------------------------------------------------------------------
# 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:
- chipseq
\ No newline at end of file
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