Newer
Older
#
# metadata for the Astrocyte CellRanger mkfastq workflow package
#
# -----------------------------------------------------------------------------
# BASIC INFORMATION
# -----------------------------------------------------------------------------
# A unique identifier for the workflow package, text/underscores only
name: 'cellranger_count'
# Who wrote this?
author: 'Gervaise Henry and Venkat Malladi'
# A contact email address for questions
email: 'bicf@utsouthwestern.edu'
# A more informative title for the workflow package
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
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
# A summary of the workflow package in plain text
description: |
This is a workflow package for the BICF/Strand Lab CellRanger count workflow system.
It implements 10x CellRanger count analysis workflow 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'
# -----------------------------------------------------------------------------
# NEXTFLOW WORKFLOW CONFIGURATION
# -----------------------------------------------------------------------------
# Remember - The workflow file is always named 'workflow/main.nf'
# The workflow must publish all final output into $baseDir
# A list of cluster environment modules that this workflow requires to run.
# Specify versioned module names to ensure reproducability.
workflow_modules:
- 'python/3.6.1-2-anaconda'
- 'cellranger/2.1.1'
- 'bcl2fastq/2.17.1.14'
# 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: |
Pairs (read1 and read2) of fastq.gz files from a sequencing of 10x single-cell expereiment. Index fastq not required.
regex: ".*fastq.gz"
min: 2
- id: designFile
type: file
required: true
regex: ".*csv"
description: |
A design file listing sample, corresponding read1 filename, corresponding read2 filename. There can be multiple rows with the same sample name, if there are multiple fastq's for that sample.
- [ '/project/apps_database/cellranger/refdata-cellranger-GRCh38-1.2.0', 'Human GRCh38']
- [ '/project/apps_database/cellranger/refdata-cellranger-hg19-1.2.0', 'Human GRCh37 (hg19)']
- [ '/project/apps_database/cellranger/refdata-cellranger-mm10-1.2.0', 'Mouse GRCm38 (mm10)']
- [ '/project/apps_database/cellranger/refdata-cellranger-hg19_and_mm10-1.2.0', 'Human GRCh37 (hg19) + Mouse GRCm38 (mm19)']
- [ '/project/apps_database/cellranger/refdata-cellranger-ercc92-1.2.0', 'ERCC.92 Spike-In']
required: true
description: |
Reference species and genome used for alignment and subsequent analysis.
- id: expectCells
type: integer
default: 3000
min: 0
max: 10000
required: false
description: |
Expected number of recovered cells.
- id: forceCells
type: integer
default: 0
min: 0
max: 10000
required: false
description: |
Force pipeline to use this number of cells, bypassing the cell detection algorithm. Use this if the number of cells estimated by Cell Ranger is not consistent with the barcode rank plot. A value of 0 ignores this option. Any value other than 0 overrides expect-cells.
# -----------------------------------------------------------------------------
# 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