/
Snakefile
180 lines (169 loc) · 5.97 KB
/
Snakefile
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
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
configfile: "config.yaml"
import os
if not os.path.exists("stderr"): os.makedirs("stderr")
if not os.path.exists("stdout"): os.makedirs("stdout")
SAMPLESPATH = config["SAMPLESPATH"]
SOURCE = os.path.dirname(SAMPLESPATH[0])
d = {}
SAMPLES = []
for eachSample in SAMPLESPATH:
basename = os.path.basename(eachSample)
SAMPLES.append(basename)
d[basename] = eachSample
rule all:
params:
error_file = "stderr/all.err",
out_file = "stdout/all.out",
run_time = "00:04:00",
memory = "40",
job_name = "all"
threads: 1
input:
expand(os.path.join("pieChart", "{sample}" + ".png"), sample=list(d.keys()))
rule unmapped_count:
input:
bam=lambda wildcards: d[wildcards.sample]
output:
readnum=os.path.join("unmapped_counts", "{sample}" + ".txt")
threads: 1
params:
error_file = lambda wildcards: "stderr/{}.count.err".format(wildcards.sample),
out_file = lambda wildcards: "stdout/{}.count.out".format(wildcards.sample),
run_time = "00:10:00",
memory = "4000",
job_name = "count"
container:
"docker://howardxu520/skipper:samtools_1.17"
shell:
"""
samtools view -cf 4 {input.bam} > {output.readnum}
echo {SOURCE} >> {output}
"""
rule unmapped_bam:
input:
info="unmapped_counts/{SAMPLES}.txt"
output:
"unmapped_counts/{SAMPLES}_unmapped_downsampled.bam"
threads: 1
params:
N_downsample_reads=config["N_downsample_reads"],
error_file = "stderr/{SAMPLES}.bam.err",
out_file = "stdout/{SAMPLES}.bam.out",
run_time = "00:20:00",
memory = "4000",
job_name = "bam"
container:
"docker://howardxu520/eclip-qc:python"
shell:
"python3 scripts/downsampled_seqs.py -input {input.info} -N_downsample {params.N_downsample_reads} -output {output}"
rule unmapped_fasta:
input:
bam="unmapped_counts/{SAMPLES}_unmapped_downsampled.bam"
output:
"unmapped_counts/{SAMPLES}_unmapped_downsampled.fasta"
threads: 1
params:
error_file = "stderr/{SAMPLES}.fasta.err",
out_file = "stdout/{SAMPLES}.fasta.out",
run_time = "00:20:00",
memory = "40000",
job_name = "fasta"
container:
"docker://howardxu520/skipper:samtools_1.17"
shell:
"samtools fasta {input.bam} > {output}"
rule unmapped_blast_synthetic:
threads: 4
params:
error_file = "stderr/{SAMPLES}.blast_synthetic.err",
out_file = "stdout/{SAMPLES}.blast_synthetic.out",
run_time = "10:00:00",
memory = "40000",
job_name = "blast_synthetic",
DB = config["DB_synthetic"],
outfmt = 6,
max_target_seqs = 5,
max_hsps = 1
input:
fasta="unmapped_counts/{SAMPLES}_unmapped_downsampled.fasta"
output:
"unmapped_counts/{SAMPLES}_unmappedblast_downsampled_blast_synthetic.tsv"
container:
"docker://howardxu520/eclip-qc:blast_2.13.0"
shell:
"blastn -db {params.DB} -query {input.fasta} -out {output} -outfmt {params.outfmt} -max_target_seqs {params.max_target_seqs} -max_hsps {params.max_hsps} -num_threads {threads}"
rule filter_synthetic:
input:
blast="unmapped_counts/{SAMPLES}_unmappedblast_downsampled_blast_synthetic.tsv",
fasta="unmapped_counts/{SAMPLES}_unmapped_downsampled.fasta"
output:
"unmapped_counts/{SAMPLES}_unmapped_downsampled_filtered.fasta"
threads: 1
params:
error_file = "stderr/{SAMPLES}.synthetic.err",
out_file = "stdout/{SAMPLES}.synthetic.out",
run_time = "10:00:00",
memory = "400",
job_name = "synthetic"
container:
"docker://howardxu520/eclip-qc:python"
shell:
"python3 scripts/filter_synthetic.py {input.blast} {input.fasta} {output}"
rule unmapped_blastn:
threads: 4
input:
fasta="unmapped_counts/{SAMPLES}_unmapped_downsampled_filtered.fasta"
params:
error_file = "stderr/{SAMPLES}.blastn.err",
out_file = "stdout/{SAMPLES}.blastn.out",
run_time = "10:00:00",
memory = "40000",
job_name = "blastn",
DB = config["DB_N"],
outfmt = 6,
max_target_seqs = 5,
max_hsps = 1
output:
"unmapped_counts/{SAMPLES}_unmappedblast_downsampled_blastn.tsv"
container:
"docker://howardxu520/eclip-qc:blast_2.13.0"
shell:
"blastn -db {params.DB} -query {input.fasta} -out {output} -outfmt {params.outfmt} -max_target_seqs {params.max_target_seqs} -max_hsps {params.max_hsps} -num_threads {threads}"
rule unmapped_blastx:
threads: 4
input:
fasta="unmapped_counts/{SAMPLES}_unmapped_downsampled_filtered.fasta"
params:
error_file = "stderr/{SAMPLES}.blastx.err",
out_file = "stdout/{SAMPLES}.blastx.out",
run_time = "10:00:00",
memory = "40000",
job_name = "blastx",
DB = config["DB_X"],
outfmt = 6,
max_target_seqs = 5,
max_hsps = 1
output:
"unmapped_counts/{SAMPLES}_unmappedblast_downsampled_blastx.tsv"
container:
"docker://howardxu520/eclip-qc:diamond"
shell:
"diamond blastx -d {params.DB} -q {input.fasta} -o {output} -k {params.max_target_seqs} --threads {threads} --max-hsps {params.max_hsps}"
rule unmapped_pie:
threads: 4
input:
input1="unmapped_counts/{SAMPLES}_unmappedblast_downsampled_blastn.tsv",
input2="unmapped_counts/{SAMPLES}_unmappedblast_downsampled_blastx.tsv",
input3="unmapped_counts/{SAMPLES}_unmappedblast_downsampled_blast_synthetic.tsv",
output:
"pieChart/{SAMPLES}.png"
params:
error_file = "stderr/{SAMPLES}.pie.err",
out_file = "stdout/{SAMPLES}.pie.out",
memory = "4000",
run_time = "10:00:00",
job_name = "pie"
container:
"docker://howardxu520/eclip-qc:python"
shell:
"python3 scripts/blastresults_piechart.py {input.input1} {input.input2} {output}"