-
Notifications
You must be signed in to change notification settings - Fork 0
/
seekdeep_nanopore_general_experimental.smk
130 lines (126 loc) · 4.64 KB
/
seekdeep_nanopore_general_experimental.smk
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
130
configfile: 'seekdeep_nanopore_general_experimental.yaml'
rule all:
input:
analysis_done=config['output_folder']+'/finished_analysis.txt',
out_snakefile=config['output_folder']+'/seekdeep_nanopore_general_experimental.smk',
out_config_file=config['output_folder']+'/seekdeep_nanopore_general_experimental.yaml'
rule copy_files:
'''
copies snakemake script and config files to output folder for reproducibility.
'''
input:
in_snakefile='seekdeep_nanopore_general_experimental.smk',
in_config_file='seekdeep_nanopore_general_experimental.yaml'
output:
out_snakefile=config['output_folder']+'/seekdeep_nanopore_general_experimental.smk',
out_config_file=config['output_folder']+'/seekdeep_nanopore_general_experimental.yaml'
shell:
'''
cp {input.in_snakefile} {output.out_snakefile}
cp {input.in_config_file} {output.out_config_file}
'''
rule genTargetInfoFromGenomes:
input:
data_folder=config['primer_plus_fastq_binding'],
genome_root_folder=config['genome_binding'],
sif_file=config['sif_file_location']
params:
output_dir=config['output_folder'],
primer_file=config['primer_file'],
gff_subfolder=config['gff_subfolder'],
genome_subfolder=config['genome_subfolder'],
extra_args=config['extra_gen_target_info_cmds']
output:
primer_info=config['output_folder']+'/extractedRefSeqs/locationsByGenome/Pf3D7_infos.tab.txt'
threads: config['cpus_to_use']
resources:
time_min=config['max_run_time_min'],
mem_mb=config['max_memory_mb'],
nodes=config['cpus_to_use']
shell:
'''
singularity exec \
-B {input.genome_root_folder}:/genome_info \
-B {input.data_folder}:/input_data \
-B {params.output_dir}:/seekdeep_output \
{input.sif_file} SeekDeep genTargetInfoFromGenomes \
--primers /input_data/{params.primer_file} \
--longRangeAmplicon \
--useBlast \
--genomeDir /genome_info/{params.genome_subfolder} \
--gffDir /genome_info/{params.gff_subfolder} \
{params.extra_args} \
--dout /seekdeep_output/extractedRefSeqs \
--overWriteDir \
--numThreads {threads} \
--shortNames
'''
rule setupTarAmpAnalysis:
input:
data_folder=config['primer_plus_fastq_binding'],
sif_file=config['sif_file_location'],
primer_info=config['output_folder']+'/extractedRefSeqs/locationsByGenome/Pf3D7_infos.tab.txt'
params:
output_dir=config['output_folder'],
primer_file=config['primer_file'],
fastq_folder=config['fastq_subfolder'],
for_seekdeep='/seekdeep_output/extractedRefSeqs/forSeekDeep',
softlink_fastq_binding=config['softlink_fastq_binding'],
extra_extractor_cmds=config['extra_extractor_cmds'],
extra_kluster_cmds=config['extra_kluster_cmds'],
extra_process_cluster_cmds=config['extra_process_cluster_cmds']
output:
setup_done=config['output_folder']+'/finished_setup.txt'
threads: config['cpus_to_use']
shell:
'''
singularity exec \
-B {input.data_folder}:/input_data \
-B {params.output_dir}:/seekdeep_output \
{params.softlink_fastq_binding} \
{input.sif_file} SeekDeep setupTarAmpAnalysis \
--outDir /seekdeep_output/analysis \
--technology nanopore \
--uniqueKmersPerTarget {params.for_seekdeep}/uniqueKmers.tab.txt.gz \
--inputDir /input_data/{params.fastq_folder} \
--idFile /input_data/{params.primer_file} \
--lenCutOffs {params.for_seekdeep}/lenCutOffs.txt \
--doNotGuessRecFlags {params.extra_extractor_cmds} \
{params.extra_kluster_cmds} \
{params.extra_process_cluster_cmds} \
--previousPopSeqsDir {params.for_seekdeep}/refSeqs/ \
--numThreads {threads}
touch {output.setup_done}
'''
rule runAnalysis:
input:
data_folder=config['primer_plus_fastq_binding'],
sif_file=config['sif_file_location'],
setup_done=config['output_folder']+'/finished_setup.txt',
genome_root_folder=config['genome_binding']
params:
output_dir=config['output_folder'],
softlink_fastq_binding=config['softlink_fastq_binding'],
junk_file1=temp('junk_file1.sh'),
junk_file2=temp('junk_file2.sh'),
junk_file3=temp('junk_file3.sh'),
output:
analysis_done=config['output_folder']+'/finished_analysis.txt'
threads: config['cpus_to_use']
resources:
time_min=config['max_run_time_min'],
mem_mb=config['max_memory_mb'],
nodes=config['cpus_to_use']
shell:
'''
echo "cd /home/analysis" >{params.junk_file1}
echo "./runAnalysis.sh" >{params.junk_file2}
cat {params.junk_file1} {params.junk_file2} >{params.junk_file3}
singularity exec -B {input.data_folder}:/input_data \
-B {params.output_dir}:/seekdeep_output \
-B {input.genome_root_folder}:/genome_info \
{params.softlink_fastq_binding} \
-B {params.output_dir}/analysis/:/home/analysis \
{input.sif_file} bash {params.junk_file3} {threads}
touch {output.analysis_done}
'''