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#
# metadata for the example astrocyte ChipSeq workflow package
#

# -----------------------------------------------------------------------------
# BASIC INFORMATION
# -----------------------------------------------------------------------------

# A unique identifier for the workflow package, text/underscores only
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name: 'rnaseq_variant_bicf'
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# Who wrote this?
author: 'Brandi Cantarel'
# A contact email address for questions
email: 'biohpc-help@utsouthwestern.edu'
# A more informative title for the workflow package
title: 'BICF RNASeq Variant Analysis Workflow'
# A summary of the workflow package in plain text
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description: 'THIS WORKFLOW IS OBSOLETE!  The Main BICF workflow includes variant analysis and differential expression analysis as one easy to use workflow.'
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# -----------------------------------------------------------------------------
# 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.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:
  - 'bcftools/intel/1.3'
  - 'bedtools/2.25.0'
  - 'bwa/intel/0.7.12'
  - 'gatk/3.5'
  - 'picard/1.127'
  - 'integrate/0.2.6'
  - 'samtools/intel/1.3'
  - 'snpeff/4.2'
  - 'speedseq/20160506'
  - 'vcftools/0.1.11'
  - 'jags/4.2.0'

# 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:

86
  - id: bamrna
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    type: files
    required: true
    description: |
      Alignment files from a RNASeq experiment
    min: 1
 
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  - id: bamdna
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    type: files
    required: false
    description: |
      BAM Files from Genomic Sequence from the same samples used for Gene Fusion Analysis

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  - id: incdna
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    type: select
    required: true
    choices:
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      - [ '0', 'Use Only RNA for Fusion Calling']
      - [ '1', 'Include Genomics Data']
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    description: |
      DNA BAM files can be included for Gene Fusion Calling

  - id: design
    type: file
    required: true
    description: |
      A design file listing pairs of sample name and sample group

  - id: genome
    type: select
    choices:
      - [ '/project/shared/bicf_workflow_ref/GRCh38', 'Human GRCh38']
      - [ '/project/shared/bicf_workflow_ref/GRCh37', 'Human GRCh37']
      - [ '/project/shared/bicf_workflow_ref/GRCm38', 'Mouse GRCh38']
    required: true
    description: |
      Reference genome for 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: []


# # List of any Bioconductor packages, not provided by the modules, that must be made
# available to the vizapp
vizapp_bioc_packages: []