#
# 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
# 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: fastqs
type: files
required: true
description: |
One or more input paired-end FASTQ files from a RNASeq experiment
regex: ".*(fastq|fq)*"
min: 1
- id: stranded
type: select
required: true
choices:
- [ '0', 'Unstranded']
- [ '1', 'Stranded']
- [ '2', 'Reverse Stranded']
description: |
In the case that the sequence libraries where generated using a stranded specific protocol.
- id: pairs
type: select
required: true
choices:
- [ 'pe', 'Paired End']
- [ 'se', 'Single End']
description: |
In single-end sequencing, the sequencer reads a fragment from only one end to the other, generating the sequence of base pairs. In paired-end reading it starts at one read, finishes this direction at the specified read length, and then starts another round of reading from the opposite end of the fragment.
- id: align
type: select
required: true
choices:
- [ 'hisat', 'HiSAT2']
- [ 'star', 'STAR']
description: |
Alignment tool
- id: fusion
type: select
required: true
choices:
- [ 'skip', 'No Fusion Detection']
- [ 'detect', 'Fusion Detection']
description: |
Run Star Fusion
- id: markdups
type: select
required: true
choices:
- [ 'picard', 'Remove Duplicates']
- [ 'null', 'Keep All Sequences']
description: |
Duplicate reads are defined as originating from the same original fragment of DNA. Duplicates are identified as read pairs having identical 5-prime positions (coordinate and strand) for both reads in a mate pair and optionally, matching unique molecular identifier reads.
- id: dea
type: select
required: true
choices:
- [ 'detect', 'Run Statistical Analysis']
- [ 'skip', 'Skip Statistical Analysis']
description: |
Runs deSEq2 and EdgeR
- id: design
type: file
required: true
regex: ".*txt"
description: |
A design file listing pairs of sample name and sample group.
Columns must include: SampleID,SampleName,SampleGroup,FullPathToFqR1,FullPathToFqR2
- id: genome
type: select
choices:
- [ '/project/shared/bicf_workflow_ref/human/GRCh38', 'Human GRCh38']
- [ '/project/shared/bicf_workflow_ref/human/GRCh37', 'Human GRCh37']
- [ '/project/shared/bicf_workflow_ref/mouse/GRCm38', 'Mouse GRCm38']
- [ '/project/shared/bicf_workflow_ref/mouse/GRCm39', 'Mouse GRCm39']
required: true
description: |
Reference genome for alignment
- id: geneset
type: select
choices:
- ['h.all.v6.2.symbols.gmt','Hallmark Gene Sets']
- ['c2.all.v5.1.symbols.gmt','Curated Gene Sets']
- ['c3.all.v5.1.symbols.gmt','Motif Gene Sets']
- ['c5.all.v6.2.symbols.gmt','Gene Ontology Gene Sets']
- ['c6.all.v5.1.symbols.gmt','Oncogenic Signatures']
- ['c7.all.v5.1.symbols.gmt','Immunological Signatures']
required: true
description: |
Gene Set Definitions used for QuSAGE Analysis -- see http://software.broadinstitute.org/gsea/msigdb/ for geneset descriptions
# -----------------------------------------------------------------------------
# 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/3.4.1-gccmkl'
# List of any CRAN packages, not provided by the modules, that must be made
# available to the vizapp
vizapp_cran_packages:
- sqldf
- crosstalk
- htmltools
- htmlwidgets
- httpuv
- shiny
- Vennerable
- DT
- grid
- gridExtra
- ggplot2
- gplots
- gtools
- RColorBrewer
- tidyverse
# # List of any Bioconductor packages, not provided by the modules, that must be made
# available to the vizapp
vizapp_bioc_packages:
- qusage
- ballgown
- edgeR
- DESeq2
vizapp_github_packages:
- js229/Vennerable