astrocyte_pkg.yml

#
# metadata for the example astrocyte ChipSeq workflow package
#

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

# A unique identifier for the workflow package, text/underscores only
name: 'rnaseq_bicf'
# 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 Analysis Workflow'
# A summary of the workflow package in plain text
description: |
  This is a workflow package for the BioHPC/BICF RNASeq workflow system.
  It implements differential expression analysis, gene set enrichment analysis,
  gene fusion analysis and variant identification using RNASeq data.
  

# -----------------------------------------------------------------------------
# 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:
  - 'trimgalore/0.4.1'
  - 'cutadapt/1.9.1'
  - 'hisat2/2.0.1-beta-intel'
  - 'samtools/intel/1.3'
  - 'picard/1.127'
  - 'subread/1.5.0-intel'
  - 'stringtie/1.1.2-intel'
  - 'speedseq/20160506'
  - 'python/2.7.x-anaconda'
# 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