-
Notifications
You must be signed in to change notification settings - Fork 0
/
FastqToBam.wdl
287 lines (249 loc) · 7.45 KB
/
FastqToBam.wdl
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
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
version 1.0
workflow FastqToBam {
input {
String sample_name
File fastq_1
File fastq_2
Boolean clean_fastqs = false
Int n_fastq_shards = 1
#Boolean cram_out = true
#String reference_name
File reference_fasta
File reference_fasta_index
File reference_dict
File? reference_alt
File reference_sa
File reference_ann
File reference_bwt
File reference_pac
File reference_amb
# File dbSNP_vcf
# File dbSNP_vcf_index
# Array[File] known_indels_sites_VCF
# Array[File] known_indels_sites_index
# File geneList
# String permanent_bucket_path
String fastq_pair_docker = "vanallenlab/fastq-pair:latest"
String fastqsplitter_docker = "vanallenlab/fastqsplitter:latest"
String gotc_docker = "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.7-1603303710"
# String gatk_docker = "broadinstitute/gatk:latest"
# String gatk_path = "/gatk/gatk"
# String python_docker = "python:2.7"
String fastq_suffix = ".fq.gz"
Int clean_fastq_reads_per_hash_cell = 8
Int clean_fastq_disk_scaling_factor = 6
Float clean_fastq_mem_gb = 64
# Int? sort_and_fix_tags_disk_size
Float? bwa_mem_gb
Int? bwa_num_cpu
Int? bwa_disk_size
# Int? gather_bam_files_disk_size
}
# Clean up FASTQs with fastq-pair
if ( clean_fastqs ) {
call CleanFastqs {
input:
fastq_1 = fastq_1,
fastq_2 = fastq_2,
fastq_suffix = fastq_suffix,
reads_per_hash_cell = clean_fastq_reads_per_hash_cell,
disk_scaling_factor = clean_fastq_disk_scaling_factor,
mem_gb = clean_fastq_mem_gb,
docker = fastq_pair_docker
}
}
File fq1 = select_first([CleanFastqs.fq_paired_1, fastq_1])
File fq2 = select_first([CleanFastqs.fq_paired_2, fastq_2])
Array[File] fq_singles = select_first([CleanFastqs.fq_singles, []])
# Split paired fastqs to parallelize alignment
if ( n_fastq_shards > 1 ) {
call SplitFastq as SplitFq1 {
input:
fastq = fq1,
n_shards = n_fastq_shards,
docker = fastqsplitter_docker
}
call SplitFastq as SplitFq2 {
input:
fastq = fq2,
n_shards = n_fastq_shards,
docker = fastqsplitter_docker
}
}
Array[File] sharded_fq1 = select_first([SplitFq1.fq_shards, [fq1]])
Array[File] sharded_fq2 = select_first([SplitFq2.fq_shards, [fq2]])
Array[Pair[File, File]] sharded_fq_pairs = zip(sharded_fq1, sharded_fq2)
# Align paired fastqs with BWA
scatter ( fq_pair in sharded_fq_pairs ) {
call Bwa as AlignPairs {
input:
input_fastqs = [fq_pair.left, fq_pair.right],
output_basename = sample_name + "." + basename(fq_pair.left, ".fq.gz"),
ref_fasta = reference_fasta,
ref_fasta_index = reference_fasta_index,
ref_dict = reference_dict,
ref_alt = reference_alt,
ref_amb = reference_amb,
ref_ann = reference_ann,
ref_bwt = reference_bwt,
ref_pac = reference_pac,
ref_sa = reference_sa,
mem_gb = bwa_mem_gb,
num_cpu = bwa_num_cpu,
disk_size = bwa_disk_size,
docker = gotc_docker
}
}
scatter ( fastq in fq_singles ) {
call Bwa as AlignSingles {
input:
input_fastqs = [fastq],
output_basename = sample_name,
ref_fasta = reference_fasta,
ref_fasta_index = reference_fasta_index,
ref_dict = reference_dict,
ref_alt = reference_alt,
ref_amb = reference_amb,
ref_ann = reference_ann,
ref_bwt = reference_bwt,
ref_pac = reference_pac,
ref_sa = reference_sa,
mem_gb = bwa_mem_gb,
num_cpu = bwa_num_cpu,
disk_size = bwa_disk_size,
docker = gotc_docker
}
}
output {
# Merge BAMs, mark duplicates
Array[File] bams_for_gatk = flatten([AlignPairs.output_bam, AlignSingles.output_bam])
}
}
# Clean up FASTQs with fastq-pair
task CleanFastqs {
input {
File fastq_1
File fastq_2
String docker
String fastq_suffix = ".fq.gz"
Int reads_per_hash_cell = 3
Int disk_scaling_factor = 10
Float mem_gb = 31.5
}
String f1_basename = basename(fastq_1, fastq_suffix)
String f2_basename = basename(fastq_2, fastq_suffix)
Int disk_gb_base = ceil(3 * size([fastq_1, fastq_2], "GB"))
Int disk_gb = (disk_scaling_factor * disk_gb_base) + 10
command <<<
set -eu -o pipefail
# Check whether fastqs are gzipped and uncompress if necessary
if [ $( file ~{fastq_1} | fgrep gzip | wc -l ) -gt 0 ]; then
zcat ~{fastq_1} > ~{f1_basename}.fastq
else
mv ~{fastq_1} > ~{f1_basename}.fastq
fi
if [ $( file ~{fastq_2} | fgrep gzip | wc -l ) -gt 0 ]; then
zcat ~{fastq_1} > ~{f2_basename}.fastq
else
mv ~{fastq_1} > ~{f2_basename}.fastq
fi
# Get number of reads
n_reads=$( cat ~{f1_basename}.fastq | wc -l | awk '{ print $1 / 4 }' | cut -f1 -d\. )
echo -e "\nCounted $n_reads total reads\n"
# Set hash size to n_reads / reads_per_hash_cell
hash_size=$( echo $n_reads | awk -v denom=~{reads_per_hash_cell} '{ printf "%.0f\n", $1 / denom }' | cut -f1 -d\. )
echo -e "\nSetting hash size to $hash_size\n"
fastq_pair -p -t $hash_size \
~{f1_basename}.fastq \
~{f2_basename}.fastq
for out in paired single; do
gzip -f ~{f1_basename}.fastq.$out.fq
gzip -f ~{f2_basename}.fastq.$out.fq
done
>>>
output {
File fq_paired_1 = "~{f1_basename}.fastq.paired.fq.gz"
File fq_paired_2 = "~{f2_basename}.fastq.paired.fq.gz"
Array[File] fq_singles = ["~{f1_basename}.fastq.single.fq.gz",
"~{f2_basename}.fastq.single.fq.gz"]
}
runtime {
docker: docker
memory: mem_gb + " GB"
cpu: 4
disks: "local-disk " + disk_gb + " HDD"
preemptible: 5
}
}
# Evenly divide paired fastqs to parallelize alignment
task SplitFastq {
input {
File fastq
Int n_shards
String docker
}
Int disk_gb = ceil(size(fastq, "GB") * 3) + 10
String out_prefix = basename(fastq, ".fq.gz")
command <<<
set -eu -o pipefail
# Build fastqsplitter command
cmd="fastqsplitter -i ~{fastq}"
for i in $( seq 1 ~{n_shards} ); do
cmd="$cmd -o ~{out_prefix}.$i.fq.gz"
done
# Split fastqs
echo -e "Now splitting fastqs with the following command:\n$cmd\n"
eval $cmd
>>>
output {
Array[File] fq_shards = glob("~{out_prefix}.*.fq.gz")
}
runtime {
docker: docker
memory: "3.5GB"
cpu: 2
disks: "local-disk " + disk_gb + " HDD"
preemptible: 5
}
}
# Align single or paired fastqs with BWA MEM
task Bwa {
input {
Array[File] input_fastqs
String output_basename
File ref_fasta
File ref_fasta_index
File ref_dict
File? ref_alt
File ref_amb
File ref_ann
File ref_bwt
File ref_pac
File ref_sa
Float mem_gb = 32
String num_cpu = 8
Int preemptible_tries = 3
Int? disk_size
String docker
}
Int default_disk_size = ceil(3 * size(input_fastqs, "GB")) + 10
command <<<
set -eu -o pipefail
# Align fastq(s) with bwa
/usr/gitc/bwa mem -K 100000000 -v 3 -t ~{num_cpu} -Y \
~{ref_fasta} \
~{sep=" " input_fastqs} \
| samtools view -b --output-fmt-option level=2 - \
> ~{output_basename}.bam
>>>
output {
File output_bam = "~{output_basename}.bam"
}
runtime {
preemptible: preemptible_tries
docker: docker
memory: "~{mem_gb} GiB"
cpu: num_cpu
disks: "local-disk " + select_first([disk_size, default_disk_size]) + " HDD"
}
}