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mihirsamdarshimihirsamdarshi
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refactor: unify preemptible attempt configuration
- Introduced `num_preemptible_attempts` as a new input variable - Replaced individual preemptible attempts across tasks with the new unified variable - Updated configuration files to use the new unified variable
1 parent 82d5fb5 commit b8a9488

19 files changed

+40
-118
lines changed

‎inputs/templates/maxquant/config-maxquant.json

+2-1
Original file line numberDiff line numberDiff line change
@@ -5,6 +5,7 @@
55
"proteomics_maxquant.mq_disk": 500,
66
"proteomics_maxquant.mq_docker": "docker-repository/maxquant:v1660",
77
"proteomics_maxquant.mq_parameters": "gcp-parameters",
8-
"proteomics_maxquant.mq_ramGB": 380
8+
"proteomics_maxquant.mq_ramGB": 380,
9+
"proteomics_maxquant.num_preemptible_attempts": 2
910
}
1011

‎inputs/templates/msgfplus/config-msgfplus-ac-lf.json

+1-6
Original file line numberDiff line numberDiff line change
@@ -44,10 +44,5 @@
4444
"proteomics_msgfplus.wrapper_docker": "docker-repository/plexedpiper:v0.4.1",
4545
"proteomics_msgfplus.wrapper_ncpu": 8,
4646
"proteomics_msgfplus.wrapper_ramGB": 60,
47-
"proteomics_msgfplus.masic_preemptible": 2,
48-
"proteomics_msgfplus.msconvert_preemptible": 2,
49-
"proteomics_msgfplus.msgf_preemptible": 2,
50-
"proteomics_msgfplus.phrp_preemptible": 2,
51-
"proteomics_msgfplus.ascore_preemptible": 2,
52-
"proteomics_msgfplus.wrapper_preemptible": 2
47+
"proteomics_msgfplus.num_preemptible_attempts": 2
5348
}

‎inputs/templates/msgfplus/config-msgfplus-ac-tmt11.json

+1-6
Original file line numberDiff line numberDiff line change
@@ -47,10 +47,5 @@
4747
"proteomics_msgfplus.refine_prior": true,
4848
"proteomics_msgfplus.sequence_db_name": "String",
4949
"proteomics_msgfplus.unique_only": false,
50-
"proteomics_msgfplus.masic_preemptible": 2,
51-
"proteomics_msgfplus.msconvert_preemptible": 2,
52-
"proteomics_msgfplus.msgf_preemptible": 2,
53-
"proteomics_msgfplus.phrp_preemptible": 2,
54-
"proteomics_msgfplus.ascore_preemptible": 2,
55-
"proteomics_msgfplus.wrapper_preemptible": 2
50+
"proteomics_msgfplus.num_preemptible_attempts": 2
5651
}

‎inputs/templates/msgfplus/config-msgfplus-ac-tmt16.json

+1-6
Original file line numberDiff line numberDiff line change
@@ -47,10 +47,5 @@
4747
"proteomics_msgfplus.refine_prior": true,
4848
"proteomics_msgfplus.sequence_db_name": "String",
4949
"proteomics_msgfplus.unique_only": false,
50-
"proteomics_msgfplus.masic_preemptible": 2,
51-
"proteomics_msgfplus.msconvert_preemptible": 2,
52-
"proteomics_msgfplus.msgf_preemptible": 2,
53-
"proteomics_msgfplus.phrp_preemptible": 2,
54-
"proteomics_msgfplus.ascore_preemptible": 2,
55-
"proteomics_msgfplus.wrapper_preemptible": 2
50+
"proteomics_msgfplus.num_preemptible_attempts": 2
5651
}

‎inputs/templates/msgfplus/config-msgfplus-ac-tmt18.json

+1-6
Original file line numberDiff line numberDiff line change
@@ -47,10 +47,5 @@
4747
"proteomics_msgfplus.refine_prior": true,
4848
"proteomics_msgfplus.sequence_db_name": "String",
4949
"proteomics_msgfplus.unique_only": false,
50-
"proteomics_msgfplus.masic_preemptible": 2,
51-
"proteomics_msgfplus.msconvert_preemptible": 2,
52-
"proteomics_msgfplus.msgf_preemptible": 2,
53-
"proteomics_msgfplus.phrp_preemptible": 2,
54-
"proteomics_msgfplus.ascore_preemptible": 2,
55-
"proteomics_msgfplus.wrapper_preemptible": 2
50+
"proteomics_msgfplus.num_preemptible_attempts": 2
5651
}

‎inputs/templates/msgfplus/config-msgfplus-ph-lf.json

+1-6
Original file line numberDiff line numberDiff line change
@@ -44,10 +44,5 @@
4444
"proteomics_msgfplus.wrapper_docker": "docker-repository/plexedpiper:v0.4.1",
4545
"proteomics_msgfplus.wrapper_ncpu": 8,
4646
"proteomics_msgfplus.wrapper_ramGB": 60,
47-
"proteomics_msgfplus.masic_preemptible": 2,
48-
"proteomics_msgfplus.msconvert_preemptible": 2,
49-
"proteomics_msgfplus.msgf_preemptible": 2,
50-
"proteomics_msgfplus.phrp_preemptible": 2,
51-
"proteomics_msgfplus.ascore_preemptible": 2,
52-
"proteomics_msgfplus.wrapper_preemptible": 2
47+
"proteomics_msgfplus.num_preemptible_attempts": 2
5348
}

‎inputs/templates/msgfplus/config-msgfplus-ph-tmt11.json

+1-6
Original file line numberDiff line numberDiff line change
@@ -47,10 +47,5 @@
4747
"proteomics_msgfplus.refine_prior": true,
4848
"proteomics_msgfplus.sequence_db_name": "String",
4949
"proteomics_msgfplus.unique_only": false,
50-
"proteomics_msgfplus.masic_preemptible": 2,
51-
"proteomics_msgfplus.msconvert_preemptible": 2,
52-
"proteomics_msgfplus.msgf_preemptible": 2,
53-
"proteomics_msgfplus.phrp_preemptible": 2,
54-
"proteomics_msgfplus.ascore_preemptible": 2,
55-
"proteomics_msgfplus.wrapper_preemptible": 2
50+
"proteomics_msgfplus.num_preemptible_attempts": 2
5651
}

‎inputs/templates/msgfplus/config-msgfplus-ph-tmt16.json

+1-6
Original file line numberDiff line numberDiff line change
@@ -47,10 +47,5 @@
4747
"proteomics_msgfplus.refine_prior": true,
4848
"proteomics_msgfplus.sequence_db_name": "String",
4949
"proteomics_msgfplus.unique_only": false,
50-
"proteomics_msgfplus.masic_preemptible": 2,
51-
"proteomics_msgfplus.msconvert_preemptible": 2,
52-
"proteomics_msgfplus.msgf_preemptible": 2,
53-
"proteomics_msgfplus.phrp_preemptible": 2,
54-
"proteomics_msgfplus.ascore_preemptible": 2,
55-
"proteomics_msgfplus.wrapper_preemptible": 2
50+
"proteomics_msgfplus.num_preemptible_attempts": 2
5651
}

‎inputs/templates/msgfplus/config-msgfplus-ph-tmt18.json

+1-6
Original file line numberDiff line numberDiff line change
@@ -47,10 +47,5 @@
4747
"proteomics_msgfplus.refine_prior": true,
4848
"proteomics_msgfplus.sequence_db_name": "String",
4949
"proteomics_msgfplus.unique_only": false,
50-
"proteomics_msgfplus.masic_preemptible": 2,
51-
"proteomics_msgfplus.msconvert_preemptible": 2,
52-
"proteomics_msgfplus.msgf_preemptible": 2,
53-
"proteomics_msgfplus.phrp_preemptible": 2,
54-
"proteomics_msgfplus.ascore_preemptible": 2,
55-
"proteomics_msgfplus.wrapper_preemptible": 2
50+
"proteomics_msgfplus.num_preemptible_attempts": 2
5651
}

‎inputs/templates/msgfplus/config-msgfplus-pr-lf.json

+1-6
Original file line numberDiff line numberDiff line change
@@ -36,10 +36,5 @@
3636
"proteomics_msgfplus.wrapper_docker": "docker-repository/plexedpiper:v0.4.1",
3737
"proteomics_msgfplus.wrapper_ncpu": 8,
3838
"proteomics_msgfplus.wrapper_ramGB": 60,
39-
"proteomics_msgfplus.masic_preemptible": 2,
40-
"proteomics_msgfplus.msconvert_preemptible": 2,
41-
"proteomics_msgfplus.msgf_preemptible": 2,
42-
"proteomics_msgfplus.phrp_preemptible": 2,
43-
"proteomics_msgfplus.ascore_preemptible": 2,
44-
"proteomics_msgfplus.wrapper_preemptible": 2
39+
"proteomics_msgfplus.num_preemptible_attempts": 2
4540
}

‎inputs/templates/msgfplus/config-msgfplus-pr-tmt11.json

+1-6
Original file line numberDiff line numberDiff line change
@@ -41,10 +41,5 @@
4141
"proteomics_msgfplus.refine_prior": true,
4242
"proteomics_msgfplus.sequence_db_name": "String",
4343
"proteomics_msgfplus.unique_only": false,
44-
"proteomics_msgfplus.masic_preemptible": 2,
45-
"proteomics_msgfplus.msconvert_preemptible": 2,
46-
"proteomics_msgfplus.msgf_preemptible": 2,
47-
"proteomics_msgfplus.phrp_preemptible": 2,
48-
"proteomics_msgfplus.ascore_preemptible": 2,
49-
"proteomics_msgfplus.wrapper_preemptible": 2
44+
"proteomics_msgfplus.num_preemptible_attempts": 2
5045
}

‎inputs/templates/msgfplus/config-msgfplus-pr-tmt16.json

+1-6
Original file line numberDiff line numberDiff line change
@@ -41,10 +41,5 @@
4141
"proteomics_msgfplus.refine_prior": true,
4242
"proteomics_msgfplus.sequence_db_name": "String",
4343
"proteomics_msgfplus.unique_only": false,
44-
"proteomics_msgfplus.masic_preemptible": 2,
45-
"proteomics_msgfplus.msconvert_preemptible": 2,
46-
"proteomics_msgfplus.msgf_preemptible": 2,
47-
"proteomics_msgfplus.phrp_preemptible": 2,
48-
"proteomics_msgfplus.ascore_preemptible": 2,
49-
"proteomics_msgfplus.wrapper_preemptible": 2
44+
"proteomics_msgfplus.num_preemptible_attempts": 2
5045
}

‎inputs/templates/msgfplus/config-msgfplus-pr-tmt18.json

+1-6
Original file line numberDiff line numberDiff line change
@@ -41,10 +41,5 @@
4141
"proteomics_msgfplus.refine_prior": true,
4242
"proteomics_msgfplus.sequence_db_name": "String",
4343
"proteomics_msgfplus.unique_only": false,
44-
"proteomics_msgfplus.masic_preemptible": 2,
45-
"proteomics_msgfplus.msconvert_preemptible": 2,
46-
"proteomics_msgfplus.msgf_preemptible": 2,
47-
"proteomics_msgfplus.phrp_preemptible": 2,
48-
"proteomics_msgfplus.ascore_preemptible": 2,
49-
"proteomics_msgfplus.wrapper_preemptible": 2
44+
"proteomics_msgfplus.num_preemptible_attempts": 2
5045
}

‎inputs/templates/msgfplus/config-msgfplus-ub-lf.json

+1-6
Original file line numberDiff line numberDiff line change
@@ -44,10 +44,5 @@
4444
"proteomics_msgfplus.wrapper_docker": "docker-repository/plexedpiper:v0.4.1",
4545
"proteomics_msgfplus.wrapper_ncpu": 8,
4646
"proteomics_msgfplus.wrapper_ramGB": 60,
47-
"proteomics_msgfplus.masic_preemptible": 2,
48-
"proteomics_msgfplus.msconvert_preemptible": 2,
49-
"proteomics_msgfplus.msgf_preemptible": 2,
50-
"proteomics_msgfplus.phrp_preemptible": 2,
51-
"proteomics_msgfplus.ascore_preemptible": 2,
52-
"proteomics_msgfplus.wrapper_preemptible": 2
47+
"proteomics_msgfplus.num_preemptible_attempts": 2
5348
}

‎inputs/templates/msgfplus/config-msgfplus-ub-tmt11.json

+1-6
Original file line numberDiff line numberDiff line change
@@ -47,10 +47,5 @@
4747
"proteomics_msgfplus.refine_prior": true,
4848
"proteomics_msgfplus.sequence_db_name": "String",
4949
"proteomics_msgfplus.unique_only": false,
50-
"proteomics_msgfplus.masic_preemptible": 2,
51-
"proteomics_msgfplus.msconvert_preemptible": 2,
52-
"proteomics_msgfplus.msgf_preemptible": 2,
53-
"proteomics_msgfplus.phrp_preemptible": 2,
54-
"proteomics_msgfplus.ascore_preemptible": 2,
55-
"proteomics_msgfplus.wrapper_preemptible": 2
50+
"proteomics_msgfplus.num_preemptible_attempts": 2
5651
}

‎inputs/templates/msgfplus/config-msgfplus-ub-tmt16.json

+1-6
Original file line numberDiff line numberDiff line change
@@ -47,10 +47,5 @@
4747
"proteomics_msgfplus.refine_prior": true,
4848
"proteomics_msgfplus.sequence_db_name": "String",
4949
"proteomics_msgfplus.unique_only": false,
50-
"proteomics_msgfplus.masic_preemptible": 2,
51-
"proteomics_msgfplus.msconvert_preemptible": 2,
52-
"proteomics_msgfplus.msgf_preemptible": 2,
53-
"proteomics_msgfplus.phrp_preemptible": 2,
54-
"proteomics_msgfplus.ascore_preemptible": 2,
55-
"proteomics_msgfplus.wrapper_preemptible": 2
50+
"proteomics_msgfplus.num_preemptible_attempts": 2
5651
}

‎inputs/templates/msgfplus/config-msgfplus-ub-tmt18.json

+1-6
Original file line numberDiff line numberDiff line change
@@ -47,10 +47,5 @@
4747
"proteomics_msgfplus.refine_prior": true,
4848
"proteomics_msgfplus.sequence_db_name": "String",
4949
"proteomics_msgfplus.unique_only": false,
50-
"proteomics_msgfplus.masic_preemptible": 2,
51-
"proteomics_msgfplus.msconvert_preemptible": 2,
52-
"proteomics_msgfplus.msgf_preemptible": 2,
53-
"proteomics_msgfplus.phrp_preemptible": 2,
54-
"proteomics_msgfplus.ascore_preemptible": 2,
55-
"proteomics_msgfplus.wrapper_preemptible": 2
50+
"proteomics_msgfplus.num_preemptible_attempts": 2
5651
}

‎wdl/proteomics_maxquant.wdl

+7-3
Original file line numberDiff line numberDiff line change
@@ -25,6 +25,7 @@ workflow proteomics_maxquant {
2525
Int mq_ramGB
2626
Int? mq_disk
2727
String mq_docker
28+
Int num_preemptible_attempts = 2
2829
}
2930

3031
call maxquant {
@@ -35,7 +36,8 @@ workflow proteomics_maxquant {
3536
disks = mq_disk,
3637
mq_parameters = mq_parameters,
3738
fasta_sequence_db = fasta_sequence_db,
38-
raw_file = raw_file
39+
raw_file = raw_file,
40+
preemptible = num_preemptible_attempts
3941
}
4042
}
4143

@@ -45,6 +47,7 @@ task maxquant {
4547
Int ramGB
4648
Int? disks
4749
String docker
50+
Int preemptible
4851
File mq_parameters
4952
File fasta_sequence_db
5053
Array[File] raw_file
@@ -97,10 +100,11 @@ task maxquant {
97100
}
98101

99102
runtime {
100-
docker: "${docker}"
103+
cpu: ncpu
101104
memory: "${ramGB} GB"
102-
cpu: "${ncpu}"
103105
disks: "local-disk ${select_first([disks, 100])} HDD"
106+
docker: "${docker}"
107+
preemptible: preemptible
104108
}
105109

106110
parameter_meta {

‎wdl/proteomics_msgfplus.wdl

+15-18
Original file line numberDiff line numberDiff line change
@@ -53,7 +53,10 @@ workflow proteomics_msgfplus {
5353
}
5454
}
5555

56-
input { # Quantification method
56+
input {
57+
Int num_preemptible_attempts = 2
58+
59+
# Quantification method
5760
String quant_method
5861

5962
# RAW INPUT FILES
@@ -66,22 +69,19 @@ workflow proteomics_msgfplus {
6669
Int masic_ramGB
6770
String masic_docker
6871
Int? masic_disk
69-
Int masic_preemptible = 2
7072
File masic_parameter
7173

7274
# MSCONVERT
7375
Int msconvert_ncpu
7476
Int msconvert_ramGB
7577
String msconvert_docker
7678
Int? msconvert_disk
77-
Int msconvert_preemptible = 2
7879

7980
# MS-GF+ SHARED OPTIONS
8081
Int msgf_ncpu
8182
Int msgf_ramGB
8283
String msgf_docker
8384
Int? msgf_disk
84-
Int msgf_preemptible = 2
8585
File fasta_sequence_db
8686
String sequence_db_name
8787

@@ -102,7 +102,6 @@ workflow proteomics_msgfplus {
102102
Int phrp_ramGB
103103
String phrp_docker
104104
Int? phrp_disk
105-
Int phrp_preemptible = 2
106105

107106
File phrp_parameter_m
108107
File phrp_parameter_t
@@ -116,15 +115,13 @@ workflow proteomics_msgfplus {
116115
Int? ascore_ramGB
117116
String? ascore_docker
118117
Int? ascore_disk
119-
Int? ascore_preemptible = 2
120118
File? ascore_parameter_p
121119

122120
# WRAPPER (PlexedPiper)
123121
Int? wrapper_ncpu
124122
Int? wrapper_ramGB
125123
String? wrapper_docker
126124
Int? wrapper_disk
127-
Int? wrapper_preemptible = 2
128125
File? sd_fractions
129126
File? sd_references
130127
File? sd_samples
@@ -142,7 +139,7 @@ workflow proteomics_msgfplus {
142139
docker = msgf_docker,
143140
disks = msgf_disk,
144141
fasta_sequence_db = fasta_sequence_db,
145-
preemptible = msgf_preemptible
142+
preemptible = num_preemptible_attempts
146143
}
147144

148145
scatter (i in range(length(raw_file))) {
@@ -152,7 +149,7 @@ workflow proteomics_msgfplus {
152149
ramGB = masic_ramGB,
153150
docker = masic_docker,
154151
disks = masic_disk,
155-
preemptible = masic_preemptible,
152+
preemptible = num_preemptible_attempts,
156153
raw_file = raw_file[i],
157154
masic_parameter = masic_parameter,
158155
quant_method = quant_method
@@ -164,7 +161,7 @@ workflow proteomics_msgfplus {
164161
ramGB = msconvert_ramGB,
165162
docker = msconvert_docker,
166163
disks = msconvert_disk,
167-
preemptible = msconvert_preemptible,
164+
preemptible = num_preemptible_attempts,
168165
raw_file = raw_file[i]
169166
}
170167

@@ -174,7 +171,7 @@ workflow proteomics_msgfplus {
174171
ramGB = msgf_ramGB,
175172
docker = msgf_docker,
176173
disks = msgf_disk,
177-
preemptible = msgf_preemptible,
174+
preemptible = num_preemptible_attempts,
178175
input_mzml = msconvert.mzml,
179176
fasta_sequence_db = fasta_sequence_db,
180177
sequencedb_files = msgf_sequences.sequencedb_files,
@@ -187,7 +184,7 @@ workflow proteomics_msgfplus {
187184
ramGB = msconvert_ramGB,
188185
docker = msconvert_docker,
189186
disks = msconvert_disk,
190-
preemptible = msconvert_preemptible,
187+
preemptible = num_preemptible_attempts,
191188
input_mzml = msconvert.mzml,
192189
input_mzid = msgf_tryptic.mzid
193190
}
@@ -198,7 +195,7 @@ workflow proteomics_msgfplus {
198195
ramGB = msconvert_ramGB,
199196
docker = ppm_errorcharter_docker,
200197
disks = msconvert_disk,
201-
preemptible = msconvert_preemptible,
198+
preemptible = num_preemptible_attempts,
202199
input_fixed_mzml = msconvert_mzrefiner.mzml_fixed,
203200
input_mzid = msgf_tryptic.mzid
204201
}
@@ -209,7 +206,7 @@ workflow proteomics_msgfplus {
209206
ramGB = msgf_ramGB,
210207
docker = msgf_docker,
211208
disks = msgf_disk,
212-
preemptible = msgf_preemptible,
209+
preemptible = num_preemptible_attempts,
213210
input_fixed_mzml = msconvert_mzrefiner.mzml_fixed,
214211
fasta_sequence_db = fasta_sequence_db,
215212
sequencedb_files = msgf_sequences.sequencedb_files,
@@ -222,7 +219,7 @@ workflow proteomics_msgfplus {
222219
ramGB = msconvert_ramGB,
223220
docker = mzidtotsvconverter_docker,
224221
disks = msconvert_disk,
225-
preemptible = msconvert_preemptible,
222+
preemptible = num_preemptible_attempts,
226223
input_mzid_final = msgf_identification.mzid_final
227224
}
228225

@@ -232,7 +229,7 @@ workflow proteomics_msgfplus {
232229
ramGB = phrp_ramGB,
233230
docker = phrp_docker,
234231
disks = phrp_disk,
235-
preemptible = phrp_preemptible,
232+
preemptible = num_preemptible_attempts,
236233
input_tsv = mzidtotsvconverter.tsv,
237234
phrp_parameter_m = phrp_parameter_m,
238235
phrp_parameter_t = phrp_parameter_t,
@@ -249,7 +246,7 @@ workflow proteomics_msgfplus {
249246
ramGB = select_first([ascore_ramGB]),
250247
docker = select_first([ascore_docker]),
251248
disks = ascore_disk,
252-
preemptible = select_first([ascore_preemptible]),
249+
preemptible = num_preemptible_attempts,
253250
input_syn = phrp.syn,
254251
input_fixed_mzml = msgf_identification.rename_mzmlfixed,
255252
ascore_parameter_p = select_first([ascore_parameter_p]),
@@ -266,7 +263,7 @@ workflow proteomics_msgfplus {
266263
ramGB = select_first([wrapper_ramGB]),
267264
docker = select_first([wrapper_docker]),
268265
disks = wrapper_disk,
269-
preemptible = select_first([wrapper_preemptible]),
266+
preemptible = num_preemptible_attempts,
270267
fractions = select_first([sd_fractions]),
271268
references = select_first([sd_references]),
272269
samples = select_first([sd_samples]),

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