forked from melbournebioinformatics/variant_calling_pipeline
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathpipeline_dev_config.py
129 lines (123 loc) · 6.99 KB
/
pipeline_dev_config.py
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
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
# This section is used by the variant calling pipeline.py to specify input data and
# working directories.
#
# Note that if you have downloaded the pipeline the directory names below are examples
# only and you will need to edit them to suit your needs.
#
# Required variables:
# - fastq_dirs: a list of directories where the raw input data is found. Currently this
# data is expected to be paired-end gzipped fastq and to follow a specific naming
# convention (see below).
# - fastq_symlink_dir: symlinks to all raw fastq files will be written to this directory
# and used by the rest of the pipeline. These symlinks have standardised names and
# are a useful flattened summary of all known input data.
# - output_dir: the directory used by the pipeline for output and intermediate files.
# A directory structure will be created under this directory by pipeline.py.
#
# Input data naming convention:
# The input fastq files must follow a naming convention so that the pipeline can determine
# the metadata fields. This convention in the default script is to use the regex
# ([a-zA-Z0-9-.]+)_([^_/]+)_[CAGTN]+_L([0-9]+)_R(1|2).fastq.gz
# This corresponds to metadata fields
# SAMPLE_RUN_TAG_LANE_READPAIR.fastq.gz
# where
# SAMPLE is a unique identifier for the sample sequenced
# RUN is a unique identifier for the experiment (e.g. run or flowcell ID)
# TAG is the barcode sequence used for multiplexing (NA if none)
# LANE is the flowcell lane identifier, written like L001
# READPAIR identifies whether the file contains forward or reverse reads, R1 or R2
#
# For example: Sample395_C0WK7ACXX_ACTTGA_L007_R1.fastq.gz
#
# This file naming convention follows that returned by many sequencing centres for
# Illumina data.
#
working_files = {
'fastq_dirs': [
'./example_data/input_data_wgs'
],
'fastq_symlink_dir': './example_data/output_wgs/fastq_symlinks',
'output_dir': './example_data/output_wgs'
}
# This section is used by the variant calling pipeline.py to specify reference data files.
#
# Note that if you have downloaded the pipeline the filenames below are examples only and
# you will need to get the relevant reference files for your data. Exactly which files
# you need depend on your data. At time of writing reference data can be obtained from:
# - Reference genome: many sources depending on data. For our human data we used the
# 1000 genomes version of the b37 (hg19) genome build, found at
# ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/human_g1k_v37.fasta.gz
# Note that your genome must use the same chromosome naming convention as any other
# reference files (such as dbSNP); if you use hg19 (chr1,chr2) instead of b37 (1,2)
# you may need to convert the files suggested below.
# - dbSNP variants: dbSNP is at http://www.ncbi.nlm.nih.gov/projects/SNP/
# A useful release summary is at http://www.ncbi.nlm.nih.gov/projects/SNP/snp_summary.cgi
# We used human variants which were obtained in VCF format from
# ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz
# - known indels for local realignment: these follow the Broad recommendations for the
# GATK tool suite and come from the GATK resource bundle. See
# http://gatkforums.broadinstitute.org/discussion/1213/what-s-in-the-resource-bundle-and-how-can-i-get-it
#
# Expected variables (if you use the relevant pipeline steps):
# - fasta_reference: the reference genome fasta. Should be in the same location as the
# .fai files produced by samtools faidx.
# TODO: do this indexing as part of the pipeline and check for index files.
# - bwa_reference: the reference genome fasta. Should be in the same location as the
# index files produced by bwa index.
# TODO: do this indexing as part of the pipeline and check for index files.
# - dbsnp: the dbSNP variants file in VCF format, for annotating variants and for
# GATK base quality recalibration.
# - indels_realign_goldstandard and
# - indels_realign_1000G: files of known indels for use in GATK local realignment.
# Currently the Broad Institute recommends using these two files (see above).
ref_files = {
'fasta_reference': '/vlsci/VR0002/shared/Reference_Files/Indexed_Ref_Genomes/bwa_Indexed/human_g1k_v37.fasta',
'bwa_reference': '/vlsci/VR0002/shared/Reference_Files/Indexed_Ref_Genomes/bwa_Indexed/human_g1k_v37.fasta',
'dbsnp': '/vlsci/VR0002/shared/Reference_Files/SNP_db/dbSNP137.vcf',
'indels_realign_goldstandard': '/vlsci/VR0002/shared/Reference_Files/Indels_for_realignment/Mills_and_1000G_gold_standard.indels.b37.vcf',
'indels_realign_1000G': '/vlsci/VR0002/shared/Reference_Files/Indels_for_realignment/1000G_phase1.indels.b37.vcf'
}
# pipeline should hold configuration options for Rubra and for the pipeline.
# This section is required for every Rubra pipeline,
# but restrict_samples and allowed_samples are specific to the variant-calling pipeline.
#
# Rubra variables:
# - logDir: the directory where batch queue scripts, stdout and sterr dumps are stored.
# - logFile: the file used to log all jobs that are run.
# - style: the default style, one of 'flowchart', 'print', 'run', 'touchfiles'. Can be
# overridden by specifying --style on the command line.
# - procs: the number of python processes to run simultaneously. This determines the
# maximum parallelism of the pipeline. For distributed jobs it also constrains the
# maximum total jobs submitted to the queue at any one time.
# - verbosity: one of 0 (quiet), 1 (normal), 2 (chatty). Can be overridden by specifying
# --verbose on the command line.
# - end: the desired tasks to be run. Rubra will also run all tasks which are dependencies
# of these tasks. Can be overridden by specifying --end on the command line.
# - force: tasks which will be forced to run, regardless of timestamps. Can be overridden
# by supplying --force on the command line.
# - rebuild: one of 'fromstart','fromend'. Whether to calculate which dependencies will
# be rerun by working back from an end task to the latest up-to-date task, or forward
# from the earliest out-of-date task. 'fromstart' is the most conservative and
# commonly used as it brings all intermediate tasks up to date.
#
# Variant-calling pipeline variables: (TODO: move to a separate section)
# - restrict_samples: whether to restrict input files to those specified by allowd_samples
# - allowed_samples: sample names that will be run of restrict_samples is True
pipeline = {
'logDir': 'log_example_wgs',
'logFile': 'pipeline.log',
'style': 'print',
'procs': 30,
'verbose': 1,
'end': ['earlyDepthOfCoverage', 'finalDepthOfCoverage',
'fastqc',
'igvcountMergedBams', 'countDedupedBam', 'countRunBam', 'countMergedBam',
'getEnsemblAnnotations',
'collateReadCounts',
'vcfIndexSNPs', 'vcfIndexIndels'
],
'force': [],
'rebuild' : "fromstart",
'restrict_samples': False,
'allowed_samples': []
}