This repository has been archived by the owner on May 7, 2019. It is now read-only.
forked from bergeycm/NGS-map
-
Notifications
You must be signed in to change notification settings - Fork 0
/
config.mk
86 lines (70 loc) · 3.26 KB
/
config.mk
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
# -------------------------------------------------------------------------------------- #
# --- Configuration makefile of user-editable variables
# -------------------------------------------------------------------------------------- #
# All paths must be absolute or relative to the NGS-map top directory
# -------------------------------------------------------------------------------------- #
# --- Paths to input files
# -------------------------------------------------------------------------------------- #
# Individual ID (used to name files)
IND_ID=Kafue
# Paths to input reads files
# Must be in FASTQ format and end in '.fastq'
# or in gzip'd FASTQ format and end in '.fastq.gz'
# FastQC will not name the output file properly if ending is '.fq'
READ1=./data/${IND_ID}.read1.fastq
READ2=./data/${IND_ID}.read2.fastq
READ_SE=./data/${IND_ID}_SE.fastq
# Paired-end or single-end analysis?
# Must be either PE or SE
READ_TYPE=PE
# Paths to genomes files
# Must be in FASTA format
GENOME_FA=genomes/papAnu2/papAnu2.fa
# Figure out genome code from path to genome FASTA
GENOME_CODE=$(notdir $(basename $(GENOME_FA)))
# Common name of genome (used to name files)
GENOME_NAME=baboon
# Should results be uploaded to AWS S3? TRUE or FALSE
DO_S3_UPLOAD=FALSE
# AWS S3 bucket name for project - location to upload results
# - Unique name, 3 to 63 characters
# - One or more labels, separated by periods
# - Can contain lowercase letters, numbers, and hyphens
# - Labels must start and end with a lowercase letter or a number.
S3_PROJECT_BUCKET_NAME=pretend-project-results-bucket-name
# -------------------------------------------------------------------------------------- #
# --- Paths to external programs
# -------------------------------------------------------------------------------------- #
FASTQC=${HOME}/downloads/fastqc-0.11.5/
FASTX=${HOME}/downloads/fastx-0.0.13/
BWA=${HOME}/downloads/bwa-0.7.13/
SAMTOOLS=${HOME}/downloads/samtools-1.3.1/
BEDTOOLS=${HOME}/downloads/bedtools-2.25.0/bin/
LIFTOVER=${HOME}/downloads/kent-20160510/
PICARD=${HOME}/downloads/picard-tools-1.119/
BAMTOOLS=/share/apps/bamtools/2.3.0/intel/bin/
GATK=${HOME}/downloads/gatk-3.5/
BCFTOOLS=${HOME}/downloads/bcftools-1.3.1/
VCFTOOLS=${HOME}/downloads/vcftools-0.1.14/bin/
TABIX=${HOME}/downloads/htslib-develop/bin/
PLINK=${HOME}/downloads/plink-1.07/
# -------------------------------------------------------------------------------------- #
# --- Parameters for external programs
# -------------------------------------------------------------------------------------- #
# BWA parameters
BWA_ALN_PARAM=-t 8
# SAMtools mpileup parameters
SNP_MIN_COV=5
SNP_MAX_COV=100
# BAMtools filter parameters
MAPQUAL=0
# Should we mark duplicates? TRUE or FALSE
MARK_DUPS=FALSE
# Max number of file handles to keep open when Picard's MarkDuplicates writes to disk.
# This should be a bit lower than the per-process max number of files that can be open.
# You can find that max using command 'ulimit -n'
# This avoids the "java.io.FileNotFoundException: (Too many open files)" exception
PICARD_MARK_DUP_MAX_FILES=4000
# -------------------------------------------------------------------------------------- #
# --- Parameters for multi-sample SNP calling
# -------------------------------------------------------------------------------------- #