forked from aryarm/as_analysis
-
Notifications
You must be signed in to change notification settings - Fork 0
/
run-all.bash
executable file
·91 lines (80 loc) · 2.45 KB
/
run-all.bash
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
#!/bin/bash
#$ -t 1
#$ -q iblm.q
#$ -V
#$ -j y
#$ -cwd
# An example bash script demonstrating how to run the entire snakemake pipeline
# on an SGE cluster
# This script creates two separate log files:
# 1) log - the basic snakemake log of completed rules
# 2) qlog - a more detailed log of the progress of each rule and any errors
# you can specify a directory for all output here:
out_path="out"
mkdir -p "$out_path"
# Before running this snakemake pipeline, remember to verify that the config.yaml
# file has been appropriately completed with the required input info. In
# particular, make sure that you have created a samples.tsv file specifying
# paths to the fastq files for each of your samples.
snakemake \
--cluster "qsub -t 1 -V -q iblm.q -j y -o ${out_path}/qlog" \
-j 24 \
--config output_dir="${out_path}" \
--latency-wait 60 \
--use-conda \
-k \
--restart-times 2 \
&>"${out_path}/log"
# Individual portions of the snakemake pipeline can also be run on their own.
# See the "Snakefiles/" directory for Snakefiles of each of the following
# three portions of the pipeline (and the "configs/" directory for their
# corresponding config files):
#
#
# 1) Snakefile-variant_calling - align DNA fastq's and generate a filtered
# VCF containing heterozygous SNPs
#
# snakemake \
# -s Snakefiles/Snakefile-variant_calling \
# --configfile configs/config-variant_calling.yaml \
# --cluster "qsub -t 1 -V -q iblm.q -j y -o ${out_path}/qlog" \
# -j 24 \
# --config output_dir=${out_path} \
# --latency-wait 60 \
# --use-conda \
# -k \
# --restart-times 2 \
# >>${out_path}/log 2>&1
#
#
# 2) Snakefile-WASP - align RNA fastq's and filter using WASP to reduce
# mapping bias
#
# snakemake \
# -s Snakefiles/Snakefile-WASP \
# --configfile configs/config-WASP.yaml \
# --cluster "qsub -t 1 -V -q iblm.q -j y -o ${out_path}/qlog" \
# -j 24 \
# --config output_dir=${out_path} \
# --latency-wait 60 \
# --use-conda \
# -k \
# --restart-times 2 \
# >>${out_path}/log 2>&1
#
#
# 3) Snakefile-counts - retrieve counts of reads overlapping SNPs from BAM
# files generated in each of the previous portions of the pipeline and use
# them to find genes which demonstrate allelic imbalance
#
# snakemake \
# -s Snakefiles/Snakefile-counts \
# --configfile configs/config-counts.yaml \
# --cluster "qsub -t 1 -V -q iblm.q -j y -o ${out_path}/qlog" \
# -j 24 \
# --config output_dir=${out_path} \
# --latency-wait 60 \
# --use-conda \
# --restart-times 2 \
# -k \
# >>${out_path}/log 2>&1