dos2unix yaml to fix lint error

astrocyte_pkg.yml

-#
-# 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
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