-
Notifications
You must be signed in to change notification settings - Fork 2
/
Snakefile
166 lines (149 loc) · 4.71 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
import os
from os import path
if not workflow.overwrite_configfiles:
configfile: "config.yml"
workdir: path.join(config["workdir_top"], config["pipeline"])
WORKDIR = path.join(config["workdir_top"], config["pipeline"])
SNAKEDIR = path.dirname(workflow.snakefile)
if(config["per_transcript_plots"]):
config["per_transcript_plots"] = "true"
include: "snakelib/utils.snake"
rule dump_versions:
output:
ver = "versions.txt"
conda: "env.yml"
shell:"""
command -v conda > /dev/null && conda list > {output.ver}
"""
rule make_reference:
input:
trs = config["transcriptome"],
output:
ref = "input/reference.fas"
params:
spike = config["spikein_fasta"],
shell:"""
cp {input.trs} {output.ref}
if [ ! -z "{params.spike}" ]
then
cat {params.spike} >> {output.ref}
fi
"""
rule make_fofn:
input:
sum_dir = config["summary_dir"]
output:
fofn = "input/summaries.fofn"
shell:"""
find {input.sum_dir} -maxdepth 1 -type f -name "sequencing_summary*.txt" -print > {output.fofn}
"""
rule make_fastq:
input:
fqd = config["fastq_dir"]
output:
fastq = "input/reads.fastq"
conda: "env.yml"
shell:"""
find {input.fqd} -maxdepth 1 -type f -name "*.fastq" -exec cat {{}} \; | seqkit seq --rna2dna - | seqkit rmdup -n - > {output.fastq}
"""
rule nanopolish_index:
input:
f5dir = config["fast5_dir"],
fq = rules.make_fastq.output.fastq,
fofn = rules.make_fofn.output.fofn,
output:
fastq_index = "input/reads.fastq.index",
fastq_index_fai = "input/reads.fastq.index.fai",
fastq_index_gzi = "input/reads.fastq.index.gzi",
fastq_index_readdb = "input/reads.fastq.index.readdb",
conda: "env.yml"
shell:"""
nanopolish index -d {input.f5dir} -f {input.fofn} {input.fq}
"""
rule map_reads:
input:
fastq = rules.make_fastq.output.fastq,
ref = rules.make_reference.output.ref,
output:
aln = "alignment/aligned_reads_sorted.bam",
alni = "alignment/aligned_reads_sorted.bam.bai",
params:
mmq = config["min_mapping_qual"]
threads: config["threads"]
conda: "env.yml"
shell:"""
minimap2 -ax map-ont -t {threads} {input.ref} {input.fastq} | samtools view -b -F 2304 -q {params.mmq} | samtools sort -@ {threads} -o {output.aln};
samtools index {output.aln}
"""
rule call_tails:
input:
index = rules.nanopolish_index.output.fastq_index,
fastq = rules.make_fastq.output.fastq,
bam = rules.map_reads.output.aln,
ref = rules.make_reference.output.ref,
output:
tails = "tails/all_tails.tsv"
threads: config["threads"]
conda: "env.yml"
shell:"""
nanopolish polya -r {input.fastq} -b {input.bam} -g {input.ref} -t {threads} > {output.tails}
"""
rule filter_tails:
input:
tails = rules.call_tails.output.tails,
output:
flt = temp("tails/filtered_tails_sp.tsv"),
pdf = "reports/filtering_report.pdf",
tsv = "reports/filtering_report.tsv",
conda: "env.yml"
shell:"""
{SNAKEDIR}/scripts/filter_tails.py -i {input.tails} -o {output.flt} -r {output.pdf} -t {output.tsv}
"""
rule spikein_qc:
input:
tails = rules.filter_tails.output.flt,
output:
tsv = "tails/spikein_tails.tsv",
pdf = "reports/spikein_report.pdf",
med = "reports/spikein_medians.tsv",
dat = "tails/filtered_tails.tsv",
params:
spike = config["spikein_fasta"]
conda: "env.yml"
shell:"""
if [ ! -z "{params.spike}" ]
then
{SNAKEDIR}/scripts/spikein_qc.py -i {input.tails} -o {output.tsv} -d {output.dat} -m {output.med} -r {output.pdf} -s {params.spike}
else
touch {output.tsv} {output.pdf} {output.med}
mv {input.tails} {output.dat}
fi
"""
rule tails_report:
input:
tails = rules.spikein_qc.output.dat,
output:
pdf = "reports/tails_report.pdf",
tsv = "reports/tails_report.tsv",
params:
x = config["per_transcript_plots"]
conda: "env.yml"
shell:"""
X=""
if [ {params.x} == "true" ];
then
X="-x"
fi
{SNAKEDIR}/scripts/tails_report.py $X -i {input.tails} -m {output.tsv} -r {output.pdf}
"""
rule all:
input:
ver = rules.dump_versions.output.ver,
ref = rules.make_reference.output.ref,
sum_fofn = rules.make_fofn.output.fofn,
fastq = rules.make_fastq.output.fastq,
index = rules.nanopolish_index.output.fastq_index,
aln = rules.map_reads.output.aln,
tails = rules.call_tails.output.tails,
sp_rep = rules.spikein_qc.output.pdf,
tails_rep = rules.tails_report.output.pdf,