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 # metadata for the example astrocyte ChipSeq workflow package
# #
# ----------------------------------------------------------------------------- # -----------------------------------------------------------------------------
# BASIC INFORMATION # BASIC INFORMATION
# ----------------------------------------------------------------------------- # -----------------------------------------------------------------------------
# A unique identifier for the workflow package, text/underscores only # A unique identifier for the workflow package, text/underscores only
name: 'astrocyte_example' name: 'astrocyte_example'
# Who wrote this? # Who wrote this?
author: 'David Trudgian' author: 'David Trudgian'
# A contact email address for questions # A contact email address for questions
email: 'biohpc-help@utsouthwestern.edu' email: 'biohpc-help@utsouthwestern.edu'
# A more informative title for the workflow package # A more informative title for the workflow package
title: 'Astrocyte Example ChIPSeq Workflow' title: 'Astrocyte Example ChIPSeq Workflow'
# A summary of the workflow package in plain text # A summary of the workflow package in plain text
description: | description: |
This is an example workflow package for the BioHPC astrocyte workflow system. 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 It implements a simple ChIPSeq analysis workflow using BWA and MACS, plus a
simple R Shiny visualization application. simple R Shiny visualization application.
# ----------------------------------------------------------------------------- # -----------------------------------------------------------------------------
# DOCUMENTATION # DOCUMENTATION
# ----------------------------------------------------------------------------- # -----------------------------------------------------------------------------
# A list of documentation file in .md format that should be viewable from the # 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 # 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 # 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' ] # To supply a title for documentation use a pair of [ 'filename', 'title' ]
documentation_files: documentation_files:
- [ 'index.md', 'ChIPSeq Example' ] - [ 'index.md', 'ChIPSeq Example' ]
# ----------------------------------------------------------------------------- # -----------------------------------------------------------------------------
# NEXTFLOW WORKFLOW CONFIGURATION # NEXTFLOW WORKFLOW CONFIGURATION
# ----------------------------------------------------------------------------- # -----------------------------------------------------------------------------
# Remember - The workflow file is always named 'workflow/main.f' # Remember - The workflow file is always named 'workflow/main.f'
# The workflow must publish all final output into $baseDir # The workflow must publish all final output into $baseDir
# A list of clueter environment modules that this workflow requires to run. # A list of clueter environment modules that this workflow requires to run.
# Specify versioned module names to ensure reproducability. # Specify versioned module names to ensure reproducability.
workflow_modules: workflow_modules:
- 'BWA/0.7.5' - 'BWA/0.7.5'
- 'picard/1.127' - 'picard/1.127'
- 'macs/1.4.2' - 'macs/1.4.2'
# A list of parameters used by the workflow, defining how to present them, # A list of parameters used by the workflow, defining how to present them,
# options etc in the web interface. For each parameter: # options etc in the web interface. For each parameter:
# #
# REQUIRED INFORMATION # REQUIRED INFORMATION
# id: The name of the parameter in the NEXTFLOW workflow # id: The name of the parameter in the NEXTFLOW workflow
# type: The type of the parameter, one of: # type: The type of the parameter, one of:
# string - A free-format string # string - A free-format string
# integer - An integer # integer - An integer
# real - A real number # real - A real number
# file - A single file from user data # file - A single file from user data
# files - One or more files from user data # files - One or more files from user data
# select - A selection from a list of values # select - A selection from a list of values
# required: true/false, must the parameter be entered/chosen? # required: true/false, must the parameter be entered/chosen?
# description: A user friendly description of the meaning of the parameter # description: A user friendly description of the meaning of the parameter
# #
# OPTIONAL INFORMATION # OPTIONAL INFORMATION
# default: A default value for the parameter (optional) # default: A default value for the parameter (optional)
# min: Minium value/characters/files for number/string/files types # min: Minium value/characters/files for number/string/files types
# max: Maxumum 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 # regex: A regular expression that describes valid entries / filenames
# #
# SELECT TYPE # SELECT TYPE
# choices: A set of choices presented to the user for the parameter. # choices: A set of choices presented to the user for the parameter.
# Each choice is a pair of value and description, e.g. # Each choice is a pair of value and description, e.g.
# #
# choices: # choices:
# - [ 'myval', 'The first option'] # - [ 'myval', 'The first option']
# - [ 'myval', 'The second option'] # - [ 'myval', 'The second option']
# #
# NOTE - All parameters are passed to NEXTFLOW as strings... but they # NOTE - All parameters are passed to NEXTFLOW as strings... but they
# are validated by astrocyte using the information provided above # are validated by astrocyte using the information provided above
workflow_parameters: workflow_parameters:
- id: fastq - id: fastq
type: files type: files
required: true required: true
description: | description: |
One or more input FASTQ files from a ChIPSeq experiment One or more input FASTQ files from a ChIPSeq experiment
regex: ".*(fastq|fq)" regex: ".*(fastq|fq)"
min: 1 min: 1
- id: index - id: index
type: select type: select
choices: choices:
- [ '/project/apps_database/iGenomes/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/genome.fa', 'UCSC hg38'] - [ '/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/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/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/mm10/Sequence/BWAIndex/genome.fa', 'UCSC mm10']
- [ '/project/apps_database/iGenomes/Mus_musculus/UCSC/mm9/Sequence/BWAIndex/genome.fa', 'UCSC mm9'] - [ '/project/apps_database/iGenomes/Mus_musculus/UCSC/mm9/Sequence/BWAIndex/genome.fa', 'UCSC mm9']
required: true required: true
description: | description: |
Reference genome for BWA alignment Reference genome for BWA alignment
# ----------------------------------------------------------------------------- # -----------------------------------------------------------------------------
# SHINY APP CONFIGURATION # SHINY APP CONFIGURATION
# ----------------------------------------------------------------------------- # -----------------------------------------------------------------------------
# Remember - The vizapp is always 'vizapp/server.R' 'vizapp/ui.R' # Remember - The vizapp is always 'vizapp/server.R' 'vizapp/ui.R'
# The workflow must publish all final output into $baseDir # The workflow must publish all final output into $baseDir
# Name of the R module that the vizapp will run against # Name of the R module that the vizapp will run against
vizapp_r_module: 'R/3.2.1-Intel' vizapp_r_module: 'R/3.2.1-Intel'
# List of any CRAN packages, not provided by the modules, that must be made # List of any CRAN packages, not provided by the modules, that must be made
# available to the vizapp # available to the vizapp
vizapp_cran_packages: vizapp_cran_packages:
- shiny - shiny
- shinyFiles - shinyFiles
# # List of any Bioconductor packages, not provided by the modules, that must be made # # List of any Bioconductor packages, not provided by the modules, that must be made
# available to the vizapp # available to the vizapp
vizapp_bioc_packages: vizapp_bioc_packages:
- chipseq - chipseq
\ No newline at end of file
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment