Newer
Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
#
# metadata for the example astrocyte ChipSeq workflow package
#
# -----------------------------------------------------------------------------
# BASIC INFORMATION
# -----------------------------------------------------------------------------
# A unique identifier for the workflow package, text/underscores only
name: 'chipseq_analysis_bicf'
# Who wrote this?
author: 'Beibei Chen'
# A contact email address for questions
email: 'biohpc-help@utsouthwestern.edu'
# A more informative title for the workflow package
title: 'BICF ChIP-seq Analysis Workflow'
# A summary of the workflow package in plain text
description: |
This is a workflow package for the BioHPC/BICF ChIP-seq workflow system.
It implements a simple ChIP-seq analysis workflow using deepTools, Diffbind, ChipSeeker and MEME-ChIP, 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
documentation_files:
- ['index.md', 'chipseq-analysis']
# -----------------------------------------------------------------------------
# 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:
- 'deeptools/2.3.5'
- 'meme/4.11.1-gcc-openmpi'
# 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: bams
type: files
required: true
description: |
Bam files of all samples
- id: peaks
type: files
required: true
description: |
Peak files of all samples. Peaks should be sorted. Bed format
- id: design
type: files
required: true
regex: ".*(csv)"
description: |
A design file listing pairs of sample name and sample group. Must be in csv format
Columns must include: SampleID,Tissue, Factor, Condition, Replicate, Peaks, bamReads, bamControl, ControlID, PeakCaller
- [ '/project/shared/bicf_workflow_ref/GRCh38', 'human GRCh38']
- [ '/project/shared/bicf_workflow_ref/GRCh37', 'human GRCh37']
- [ '/project/shared/bicf_workflow_ref/GRCm38', 'mouse GRCm38']
required: true
description: |
Reference genome for annotation
type: integer
required: true
description: |
The number of top peaks to use for motif discovery.
# -----------------------------------------------------------------------------
# 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:
- qusage
# - ballgown
vizapp_github_packages:
- js229/Vennerable