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awgymerawgymer
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Update DEEPVARIANT/* to 1.10.0 (#11743)
* feat(deepvariant): update all modules to use v1.10.0 by default. Add explicit MPLCONFIGDIR to avoid issues with matplotlib. * feat(deepvariant): update subworkflow tests to account for required parameter change for small models arg with v1.10.0
1 parent 8b798ea commit 29031bf

12 files changed

Lines changed: 100 additions & 87 deletions

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‎modules/nf-core/deepvariant/callvariants/main.nf‎

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@ process DEEPVARIANT_CALLVARIANTS {
44
label 'process_high'
55

66
//Conda is not supported at the moment
7-
container "docker.io/google/deepvariant:1.9.0"
7+
container "docker.io/google/deepvariant:1.10.0"
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input:
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tuple val(meta), path(make_examples_tfrecords)
@@ -34,6 +34,9 @@ process DEEPVARIANT_CALLVARIANTS {
3434
def examples_tfrecords_logical_name = "${examples_tfrecord_name}@${shardCount}.gz"
3535

3636
"""
37+
export MPLCONFIGDIR=\$PWD/.matplotlib
38+
mkdir -p \$MPLCONFIGDIR
39+
3740
/opt/deepvariant/bin/call_variants \\
3841
${args} \\
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--outfile "${prefix}.call.tfrecord.gz" \\

‎modules/nf-core/deepvariant/callvariants/tests/main.nf.test.snap‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -25,7 +25,7 @@
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[
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"DEEPVARIANT_CALLVARIANTS",
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"deepvariant",
28-
"1.9.0"
28+
"1.10.0"
2929
]
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],
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"call_variants_tfrecords": [
@@ -41,7 +41,7 @@
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[
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"DEEPVARIANT_CALLVARIANTS",
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"deepvariant",
44-
"1.9.0"
44+
"1.10.0"
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]
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]
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}
@@ -50,6 +50,6 @@
5050
"nf-test": "0.9.3",
5151
"nextflow": "25.10.2"
5252
},
53-
"timestamp": "2026-02-02T17:02:54.403068431"
53+
"timestamp": "2026-05-22T12:24:48.518831"
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}
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}

‎modules/nf-core/deepvariant/callvariants/tests/nextflow.config‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -6,6 +6,6 @@ process {
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}
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process {
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withName: "DEEPVARIANT_MAKEEXAMPLES" {
9-
ext.args = '--checkpoint "/opt/models/wgs" --call_small_model_examples --small_model_indel_gq_threshold "30" --small_model_snp_gq_threshold "25" --small_model_vaf_context_window_size "51" --trained_small_model_path "/opt/smallmodels/wgs"'
9+
ext.args = '--checkpoint "/opt/models/wgs" --call_small_model_examples --small_model_indel_gq_threshold "30" --small_model_snp_gq_threshold "25" --small_model_vaf_context_window_size "51" --trained_small_model_path "/opt/smallmodels/wgs/model.keras"'
1010
}
1111
}

‎modules/nf-core/deepvariant/makeexamples/main.nf‎

Lines changed: 7 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@ process DEEPVARIANT_MAKEEXAMPLES {
33
label 'process_high'
44

55
//Conda is not supported at the moment
6-
container "docker.io/google/deepvariant:1.9.0"
6+
container "docker.io/google/deepvariant:1.10.0"
77

88
input:
99
tuple val(meta), path(input), path(index), path(intervals)
@@ -13,9 +13,9 @@ process DEEPVARIANT_MAKEEXAMPLES {
1313
tuple val(meta5), path(par_bed)
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1515
output:
16-
tuple val(meta), path("${prefix}.examples.tfrecord-*-of-*.gz{,.example_info.json}"), emit: examples
17-
tuple val(meta), path("${prefix}.gvcf.tfrecord-*-of-*.gz"), emit: gvcf
18-
tuple val(meta), path("${prefix}_call_variant_outputs.examples.tfrecord-*-of-*.gz", arity: "0..*"), emit: small_model_calls
16+
tuple val(meta), path("${prefix}.examples.tfrecord-*-of-*.gz{,.example_info.json}") , emit: examples
17+
tuple val(meta), path("${prefix}.gvcf.tfrecord-*-of-*.gz") , emit: gvcf
18+
tuple val(meta), path("${prefix}_call_variant_outputs.examples.tfrecord-*-of-*.gz", arity: "0..*"), emit: small_model_calls
1919
tuple val("${task.process}"), val('deepvariant'), eval("/opt/deepvariant/bin/run_deepvariant --version | sed 's/^.*version //'"), topic: versions, emit: versions_deepvariant
2020

2121
when:
@@ -32,6 +32,9 @@ process DEEPVARIANT_MAKEEXAMPLES {
3232
def par_regions = par_bed ? "--par_regions_bed=${par_bed}" : ""
3333

3434
"""
35+
export MPLCONFIGDIR=\$PWD/.matplotlib
36+
mkdir -p \$MPLCONFIGDIR
37+
3538
seq 0 ${task.cpus - 1} | parallel -q --halt 2 --line-buffer /opt/deepvariant/bin/make_examples \\
3639
--mode calling \\
3740
--ref "${fasta}" \\

‎modules/nf-core/deepvariant/makeexamples/tests/main.nf.test.snap‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -18,15 +18,15 @@
1818
[
1919
"DEEPVARIANT_MAKEEXAMPLES",
2020
"deepvariant",
21-
"1.9.0"
21+
"1.10.0"
2222
]
2323
]
2424
],
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"meta": {
2626
"nf-test": "0.9.3",
2727
"nextflow": "25.10.2"
2828
},
29-
"timestamp": "2026-02-02T17:09:55.034298895"
29+
"timestamp": "2026-05-22T13:06:12.609585"
3030
},
3131
"test2-examples-filenames": {
3232
"content": [
@@ -64,31 +64,31 @@
6464
[
6565
"DEEPVARIANT_MAKEEXAMPLES",
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"deepvariant",
67-
"1.9.0"
67+
"1.10.0"
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]
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]
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],
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"meta": {
7272
"nf-test": "0.9.3",
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"nextflow": "25.10.2"
7474
},
75-
"timestamp": "2026-02-02T17:07:52.050411549"
75+
"timestamp": "2026-05-22T13:05:55.381642"
7676
},
7777
"test4-versions": {
7878
"content": [
7979
[
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[
8181
"DEEPVARIANT_MAKEEXAMPLES",
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"deepvariant",
83-
"1.9.0"
83+
"1.10.0"
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]
8585
]
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],
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"meta": {
8888
"nf-test": "0.9.3",
8989
"nextflow": "25.10.2"
9090
},
91-
"timestamp": "2026-02-02T17:12:07.012233232"
91+
"timestamp": "2026-05-22T12:25:37.133164"
9292
},
9393
"test4-examples-filenames": {
9494
"content": [
@@ -111,15 +111,15 @@
111111
[
112112
"DEEPVARIANT_MAKEEXAMPLES",
113113
"deepvariant",
114-
"1.9.0"
114+
"1.10.0"
115115
]
116116
]
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],
118118
"meta": {
119119
"nf-test": "0.9.3",
120120
"nextflow": "25.10.2"
121121
},
122-
"timestamp": "2026-02-02T17:05:28.75651648"
122+
"timestamp": "2026-05-22T13:05:35.635294"
123123
},
124124
"test3-gvcf-filenames": {
125125
"content": [

‎modules/nf-core/deepvariant/makeexamples/tests/nextflow.config‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
process {
22
withName: "DEEPVARIANT_MAKEEXAMPLES" {
33
cpus = 2 // The number of output files is determined by cpus - keep it the same for tests
4-
ext.args = '--checkpoint "/opt/models/wgs" --call_small_model_examples --small_model_indel_gq_threshold "30" --small_model_snp_gq_threshold "25" --small_model_vaf_context_window_size "51" --trained_small_model_path "/opt/smallmodels/wgs"'
4+
ext.args = '--checkpoint "/opt/models/wgs" --call_small_model_examples --small_model_indel_gq_threshold "30" --small_model_snp_gq_threshold "25" --small_model_vaf_context_window_size "51" --trained_small_model_path "/opt/smallmodels/wgs/model.keras"'
55
}
66
}

‎modules/nf-core/deepvariant/postprocessvariants/main.nf‎

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@ process DEEPVARIANT_POSTPROCESSVARIANTS {
33
label 'process_medium'
44

55
//Conda is not supported at the moment
6-
container "docker.io/google/deepvariant:1.9.0"
6+
container "docker.io/google/deepvariant:1.10.0"
77

88
input:
99
tuple val(meta), path(variant_calls_tfrecord_files), path(gvcf_tfrecords), path(small_model_calls), path(intervals)
@@ -57,6 +57,9 @@ process DEEPVARIANT_POSTPROCESSVARIANTS {
5757
}
5858

5959
"""
60+
export MPLCONFIGDIR=\$PWD/.matplotlib
61+
mkdir -p \$MPLCONFIGDIR
62+
6063
/opt/deepvariant/bin/postprocess_variants \\
6164
${args} \\
6265
--ref "${fasta}" \\

‎modules/nf-core/deepvariant/postprocessvariants/tests/main.nf.test.snap‎

Lines changed: 14 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -42,7 +42,7 @@
4242
[
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"DEEPVARIANT_POSTPROCESSVARIANTS",
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"deepvariant",
45-
"1.9.0"
45+
"1.10.0"
4646
]
4747
],
4848
"gvcf": [
@@ -85,7 +85,7 @@
8585
[
8686
"DEEPVARIANT_POSTPROCESSVARIANTS",
8787
"deepvariant",
88-
"1.9.0"
88+
"1.10.0"
8989
]
9090
]
9191
}
@@ -94,7 +94,7 @@
9494
"nf-test": "0.9.3",
9595
"nextflow": "25.10.2"
9696
},
97-
"timestamp": "2026-02-02T17:22:12.888323156"
97+
"timestamp": "2026-05-22T12:26:00.102078"
9898
},
9999
"homo_sapiens - wgs": {
100100
"content": [
@@ -105,7 +105,7 @@
105105
"id": "test",
106106
"single_end": false
107107
},
108-
"test.vcf.gz:md5,707212230030c8c3efbe5c2e0428da03"
108+
"test.vcf.gz:md5,d6ec6971b53fc10bf9ed23ddf6f544c1"
109109
]
110110
],
111111
"1": [
@@ -114,7 +114,7 @@
114114
"id": "test",
115115
"single_end": false
116116
},
117-
"test.vcf.gz.tbi:md5,248648ca03f5fda904ebbef8821e0e37"
117+
"test.vcf.gz.tbi:md5,efb861c33cf51739a4ae13a2e81126b6"
118118
]
119119
],
120120
"2": [
@@ -123,7 +123,7 @@
123123
"id": "test",
124124
"single_end": false
125125
},
126-
"test.g.vcf.gz:md5,89b2e47883a65bb9cae8f173e782bb17"
126+
"test.g.vcf.gz:md5,71bf2757abd13abed78479887f9de8f6"
127127
]
128128
],
129129
"3": [
@@ -132,14 +132,14 @@
132132
"id": "test",
133133
"single_end": false
134134
},
135-
"test.g.vcf.gz.tbi:md5,1680c67fe988bc1d8220fbb4127c2c18"
135+
"test.g.vcf.gz.tbi:md5,90732f1ea2188c12fc4dab62da039f63"
136136
]
137137
],
138138
"4": [
139139
[
140140
"DEEPVARIANT_POSTPROCESSVARIANTS",
141141
"deepvariant",
142-
"1.9.0"
142+
"1.10.0"
143143
]
144144
],
145145
"gvcf": [
@@ -148,7 +148,7 @@
148148
"id": "test",
149149
"single_end": false
150150
},
151-
"test.g.vcf.gz:md5,89b2e47883a65bb9cae8f173e782bb17"
151+
"test.g.vcf.gz:md5,71bf2757abd13abed78479887f9de8f6"
152152
]
153153
],
154154
"gvcf_index": [
@@ -157,7 +157,7 @@
157157
"id": "test",
158158
"single_end": false
159159
},
160-
"test.g.vcf.gz.tbi:md5,1680c67fe988bc1d8220fbb4127c2c18"
160+
"test.g.vcf.gz.tbi:md5,90732f1ea2188c12fc4dab62da039f63"
161161
]
162162
],
163163
"vcf": [
@@ -166,7 +166,7 @@
166166
"id": "test",
167167
"single_end": false
168168
},
169-
"test.vcf.gz:md5,707212230030c8c3efbe5c2e0428da03"
169+
"test.vcf.gz:md5,d6ec6971b53fc10bf9ed23ddf6f544c1"
170170
]
171171
],
172172
"vcf_index": [
@@ -175,14 +175,14 @@
175175
"id": "test",
176176
"single_end": false
177177
},
178-
"test.vcf.gz.tbi:md5,248648ca03f5fda904ebbef8821e0e37"
178+
"test.vcf.gz.tbi:md5,efb861c33cf51739a4ae13a2e81126b6"
179179
]
180180
],
181181
"versions_deepvariant": [
182182
[
183183
"DEEPVARIANT_POSTPROCESSVARIANTS",
184184
"deepvariant",
185-
"1.9.0"
185+
"1.10.0"
186186
]
187187
]
188188
}
@@ -191,6 +191,6 @@
191191
"nf-test": "0.9.3",
192192
"nextflow": "25.10.2"
193193
},
194-
"timestamp": "2026-02-02T17:19:32.037352523"
194+
"timestamp": "2026-05-22T13:07:18.932165"
195195
}
196196
}

‎modules/nf-core/deepvariant/postprocessvariants/tests/nextflow.config‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,6 +5,6 @@ process {
55
}
66
process {
77
withName: "DEEPVARIANT_MAKEEXAMPLES" {
8-
ext.args = '--checkpoint "/opt/models/wgs" --call_small_model_examples --small_model_indel_gq_threshold "30" --small_model_snp_gq_threshold "25" --small_model_vaf_context_window_size "51" --trained_small_model_path "/opt/smallmodels/wgs"'
8+
ext.args = '--checkpoint "/opt/models/wgs" --call_small_model_examples --small_model_indel_gq_threshold "30" --small_model_snp_gq_threshold "25" --small_model_vaf_context_window_size "51" --trained_small_model_path "/opt/smallmodels/wgs/model.keras"'
99
}
1010
}

‎modules/nf-core/deepvariant/rundeepvariant/main.nf‎

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -37,6 +37,9 @@ process DEEPVARIANT_RUNDEEPVARIANT {
3737
def par_regions = par_bed ? "--par_regions_bed=${par_bed}" : ""
3838

3939
"""
40+
export MPLCONFIGDIR=\$PWD/.matplotlib
41+
mkdir -p \$MPLCONFIGDIR
42+
4043
/opt/deepvariant/bin/run_deepvariant \\
4144
--ref=${fasta} \\
4245
--reads=${input} \\
@@ -59,5 +62,6 @@ process DEEPVARIANT_RUNDEEPVARIANT {
5962
echo "stub" | gzip > ${prefix}.vcf.gz
6063
echo "stub" | gzip > ${prefix}.vcf.gz.tbi
6164
echo "stub" | gzip > ${prefix}.g.vcf.gz
62-
echo "stub" | gzip > ${prefix}.g.vcf.gz.tbi """
65+
echo "stub" | gzip > ${prefix}.g.vcf.gz.tbi
66+
"""
6367
}

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