-
Notifications
You must be signed in to change notification settings - Fork 29
/
common.wdl
353 lines (289 loc) · 8.92 KB
/
common.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
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
version 1.0
# Copyright (c) 2017 Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
task AppendToStringArray {
input {
Array[String] array
String string
String memory = "1GiB"
}
command {
echo "~{sep='\n' array}
~{string}"
}
output {
Array[String] outArray = read_lines(stdout())
}
runtime {
memory: memory
}
}
# This task will fail if the MD5sum doesn't match the file.
task CheckFileMD5 {
input {
File file
String md5
# By default cromwell expects /bin/bash to be present in the container.
# The 'bash' container does not fill this requirement. (It is in /usr/local/bin/bash)
# Use a stable version of debian:stretch-slim for this. (Smaller than ubuntu)
String memory = "1GiB"
String dockerImage = "debian@sha256:f05c05a218b7a4a5fe979045b1c8e2a9ec3524e5611ebfdd0ef5b8040f9008fa"
}
command {
bash -c '
set -e -o pipefail
echo "~{md5} ~{file}" | md5sum -c
'
}
runtime {
docker: dockerImage
memory: memory
}
}
task ConcatenateTextFiles {
input {
Array[File] fileList
String combinedFilePath
Boolean unzip = false
Boolean zip = false
String memory = "1GiB"
}
# When input and output is both compressed decompression is not needed.
String cmdPrefix = if (unzip && !zip) then "zcat " else "cat "
String cmdSuffix = if (!unzip && zip) then " | gzip -c " else ""
command {
set -e -o pipefail
mkdir -p "$(dirname ~{combinedFilePath})"
~{cmdPrefix} ~{sep=" " fileList} ~{cmdSuffix} > ~{combinedFilePath}
}
output {
File combinedFile = combinedFilePath
}
runtime {
memory: memory
}
}
task Copy {
input {
File inputFile
String outputPath
Boolean recursive = false
# Version not that important as long as it is stable.
String memory = "1GiB"
String dockerImage = "debian@sha256:f05c05a218b7a4a5fe979045b1c8e2a9ec3524e5611ebfdd0ef5b8040f9008fa"
}
command {
set -e
mkdir -p "$(dirname ~{outputPath})"
cp ~{true="-r" false="" recursive} ~{inputFile} ~{outputPath}
}
output {
File outputFile = outputPath
}
runtime {
docker: dockerImage
memory: memory
}
}
task CreateLink {
# Making this of type File will create a link to the copy of the file in
# the execution folder, instead of the actual file.
# This cannot be propperly call-cached or used within a container.
input {
String inputFile
String outputPath
String memory = "1GiB"
}
command {
ln -sf ~{inputFile} ~{outputPath}
}
output {
File link = outputPath
}
runtime {
memory: memory
}
}
task GetSamplePositionInArray {
input {
Array[String] sampleIds
String sample
# python:3.7-slim's sha256 digest. This image is based on debian buster.
String dockerImage = "python@sha256:e0f6a4df17d5707637fa3557ab266f44dddc46ebfc82b0f1dbe725103961da4e"
}
command <<<
python <<CODE
samples = ['~{sep="','" sampleIds}']
print(samples.index('~{sample}'))
CODE
>>>
output {
Int position = read_int(stdout())
}
runtime {
# 4 gigs of memory to be able to build the docker image in singularity.
memory: "4GiB"
docker: dockerImage
timeMinutes: 5
}
parameter_meta {
# inputs
sampleIds: {description: "A list of sample ids.", category: "required"}
sample: {description: "The sample for which the position is wanted.", category: "required"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
# outputs
position: {description: ""}
}
}
task MapMd5 {
input {
Map[String,String] map
String memory = "1GiB"
String dockerImage = "debian@sha256:f05c05a218b7a4a5fe979045b1c8e2a9ec3524e5611ebfdd0ef5b8040f9008fa"
}
command {
set -e -o pipefail
md5sum "~{write_map(map)}" | cut -f 1 -d ' '
}
output {
String md5sum = read_string(stdout())
}
runtime {
memory: memory
docker: dockerImage
}
}
task StringArrayMd5 {
input {
Array[String] stringArray
String memory = "1GiB"
String dockerImage = "debian@sha256:f05c05a218b7a4a5fe979045b1c8e2a9ec3524e5611ebfdd0ef5b8040f9008fa"
}
command {
set -eu -o pipefail
echo ~{sep=',' stringArray} | md5sum - | sed -e 's/ -//'
}
output {
String md5sum = read_string(stdout())
}
runtime {
memory: memory
docker: dockerImage
}
}
task TextToFile {
input {
String text
String outputFile = "out.txt"
String memory = "1GiB"
Int timeMinutes = 1
String dockerImage = "debian@sha256:f05c05a218b7a4a5fe979045b1c8e2a9ec3524e5611ebfdd0ef5b8040f9008fa"
}
command <<<
echo ~{text} > ~{outputFile}
>>>
output {
File out = outputFile
}
runtime {
memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
# inputs
text: {description: "The text to print.", category: "required"}
outputFile: {description: "The name of the output file.", category: "common"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
# outputs
out: {description: "File containing input text."}
}
}
task YamlToJson {
input {
File yaml
String outputJson = basename(yaml, "\.ya?ml$") + ".json"
String memory = "128MiB"
Int timeMinutes = 1
# biowdl-input-converter has python and pyyaml.
String dockerImage = "quay.io/biocontainers/biowdl-input-converter:0.3.0--pyhdfd78af_0"
}
command {
set -e
mkdir -p "$(dirname ~{outputJson})"
python <<CODE
import json
import yaml
with open("~{yaml}", "r") as input_yaml:
content = yaml.load(input_yaml)
with open("~{outputJson}", "w") as output_json:
json.dump(content, output_json)
CODE
}
output {
File json = outputJson
}
runtime {
memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
# inputs
yaml: {description: "The YAML file to convert.", category: "required"}
outputJson: {description: "The location the output JSON file should be written to.", category: "advanced"}
memory: {description: "The maximum amount of memory the job will need.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
# outputs
json: {description: "JSON file version of input YAML."}
}
}
struct Reference {
File fasta
File fai
File dict
}
struct IndexedVcfFile {
File file
File index
String? md5sum
}
struct IndexedBamFile {
File file
File index
String? md5sum
}
struct FastqPair {
File R1
String? R1_md5
File? R2
String? R2_md5
}
struct CaseControl {
String inputName
IndexedBamFile inputFile
String controlName
IndexedBamFile controlFile
}
struct CaseControls {
Array[CaseControl] caseControls
}