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Update DEEPVARIANT/* to 1.10.0 #11743

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Merged
awgymer merged 6 commits into from
May 27, 2026
Merged

Update DEEPVARIANT/* to 1.10.0 #11743

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e29a97c
feat(deepvariant): update all modules to use v1.10.0 by default. Add …
awgymer May 22, 2026
e043cb4
feat(deepvariant): update subworkflow tests to account for required p…
awgymer May 22, 2026
0ec2f34
Merge branch 'master' into deepvariant-1.10.0
awgymer May 27, 2026
4f2ec80
Merge branch 'master' into deepvariant-1.10.0
awgymer May 27, 2026
23ff778
Merge branch 'master' into deepvariant-1.10.0
awgymer May 27, 2026
c9f30d5
Merge branch 'master' into deepvariant-1.10.0
awgymer May 27, 2026
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5 changes: 4 additions & 1 deletion modules/nf-core/deepvariant/callvariants/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ process DEEPVARIANT_CALLVARIANTS {
label 'process_high'

//Conda is not supported at the moment
container "docker.io/google/deepvariant:1.9.0"
container "docker.io/google/deepvariant:1.10.0"

input:
tuple val(meta), path(make_examples_tfrecords)
Expand Down Expand Up @@ -34,6 +34,9 @@ process DEEPVARIANT_CALLVARIANTS {
def examples_tfrecords_logical_name = "${examples_tfrecord_name}@${shardCount}.gz"

"""
export MPLCONFIGDIR=\$PWD/.matplotlib
mkdir -p \$MPLCONFIGDIR
Comment thread
jonasscheid marked this conversation as resolved.

/opt/deepvariant/bin/call_variants \\
${args} \\
--outfile "${prefix}.call.tfrecord.gz" \\
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/deepvariant/callvariants/tests/main.nf.test.snap
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Expand Up @@ -25,7 +25,7 @@
[
"DEEPVARIANT_CALLVARIANTS",
"deepvariant",
"1.9.0"
"1.10.0"
]
],
"call_variants_tfrecords": [
Expand All @@ -41,7 +41,7 @@
[
"DEEPVARIANT_CALLVARIANTS",
"deepvariant",
"1.9.0"
"1.10.0"
]
]
}
Expand All @@ -50,6 +50,6 @@
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-02-02T17:02:54.403068431"
"timestamp": "2026-05-22T12:24:48.518831"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/deepvariant/callvariants/tests/nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,6 @@ process {
}
process {
withName: "DEEPVARIANT_MAKEEXAMPLES" {
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"'
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"'
}
}
11 changes: 7 additions & 4 deletions modules/nf-core/deepvariant/makeexamples/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ process DEEPVARIANT_MAKEEXAMPLES {
label 'process_high'

//Conda is not supported at the moment
container "docker.io/google/deepvariant:1.9.0"
container "docker.io/google/deepvariant:1.10.0"

input:
tuple val(meta), path(input), path(index), path(intervals)
Expand All @@ -13,9 +13,9 @@ process DEEPVARIANT_MAKEEXAMPLES {
tuple val(meta5), path(par_bed)

output:
tuple val(meta), path("${prefix}.examples.tfrecord-*-of-*.gz{,.example_info.json}"), emit: examples
tuple val(meta), path("${prefix}.gvcf.tfrecord-*-of-*.gz"), emit: gvcf
tuple val(meta), path("${prefix}_call_variant_outputs.examples.tfrecord-*-of-*.gz", arity: "0..*"), emit: small_model_calls
tuple val(meta), path("${prefix}.examples.tfrecord-*-of-*.gz{,.example_info.json}") , emit: examples
tuple val(meta), path("${prefix}.gvcf.tfrecord-*-of-*.gz") , emit: gvcf
tuple val(meta), path("${prefix}_call_variant_outputs.examples.tfrecord-*-of-*.gz", arity: "0..*"), emit: small_model_calls
tuple val("${task.process}"), val('deepvariant'), eval("/opt/deepvariant/bin/run_deepvariant --version | sed 's/^.*version //'"), topic: versions, emit: versions_deepvariant

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

"""
export MPLCONFIGDIR=\$PWD/.matplotlib
mkdir -p \$MPLCONFIGDIR
Comment thread
jonasscheid marked this conversation as resolved.

seq 0 ${task.cpus - 1} | parallel -q --halt 2 --line-buffer /opt/deepvariant/bin/make_examples \\
--mode calling \\
--ref "${fasta}" \\
Expand Down
16 changes: 8 additions & 8 deletions modules/nf-core/deepvariant/makeexamples/tests/main.nf.test.snap
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Expand Up @@ -18,15 +18,15 @@
[
"DEEPVARIANT_MAKEEXAMPLES",
"deepvariant",
"1.9.0"
"1.10.0"
]
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-02-02T17:09:55.034298895"
"timestamp": "2026-05-22T13:06:12.609585"
},
"test2-examples-filenames": {
"content": [
Expand Down Expand Up @@ -64,31 +64,31 @@
[
"DEEPVARIANT_MAKEEXAMPLES",
"deepvariant",
"1.9.0"
"1.10.0"
]
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-02-02T17:07:52.050411549"
"timestamp": "2026-05-22T13:05:55.381642"
},
"test4-versions": {
"content": [
[
[
"DEEPVARIANT_MAKEEXAMPLES",
"deepvariant",
"1.9.0"
"1.10.0"
]
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-02-02T17:12:07.012233232"
"timestamp": "2026-05-22T12:25:37.133164"
},
"test4-examples-filenames": {
"content": [
Expand All @@ -111,15 +111,15 @@
[
"DEEPVARIANT_MAKEEXAMPLES",
"deepvariant",
"1.9.0"
"1.10.0"
]
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-02-02T17:05:28.75651648"
"timestamp": "2026-05-22T13:05:35.635294"
},
"test3-gvcf-filenames": {
"content": [
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/deepvariant/makeexamples/tests/nextflow.config
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@@ -1,6 +1,6 @@
process {
withName: "DEEPVARIANT_MAKEEXAMPLES" {
cpus = 2 // The number of output files is determined by cpus - keep it the same for tests
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"'
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"'
}
}
5 changes: 4 additions & 1 deletion modules/nf-core/deepvariant/postprocessvariants/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ process DEEPVARIANT_POSTPROCESSVARIANTS {
label 'process_medium'

//Conda is not supported at the moment
container "docker.io/google/deepvariant:1.9.0"
container "docker.io/google/deepvariant:1.10.0"

input:
tuple val(meta), path(variant_calls_tfrecord_files), path(gvcf_tfrecords), path(small_model_calls), path(intervals)
Expand Down Expand Up @@ -57,6 +57,9 @@ process DEEPVARIANT_POSTPROCESSVARIANTS {
}

"""
export MPLCONFIGDIR=\$PWD/.matplotlib
mkdir -p \$MPLCONFIGDIR
Comment thread
jonasscheid marked this conversation as resolved.

/opt/deepvariant/bin/postprocess_variants \\
${args} \\
--ref "${fasta}" \\
Expand Down
28 changes: 14 additions & 14 deletions modules/nf-core/deepvariant/postprocessvariants/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@
[
"DEEPVARIANT_POSTPROCESSVARIANTS",
"deepvariant",
"1.9.0"
"1.10.0"
]
],
"gvcf": [
Expand Down Expand Up @@ -85,7 +85,7 @@
[
"DEEPVARIANT_POSTPROCESSVARIANTS",
"deepvariant",
"1.9.0"
"1.10.0"
]
]
}
Expand All @@ -94,7 +94,7 @@
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-02-02T17:22:12.888323156"
"timestamp": "2026-05-22T12:26:00.102078"
},
"homo_sapiens - wgs": {
"content": [
Expand All @@ -105,7 +105,7 @@
"id": "test",
"single_end": false
},
"test.vcf.gz:md5,707212230030c8c3efbe5c2e0428da03"
"test.vcf.gz:md5,d6ec6971b53fc10bf9ed23ddf6f544c1"
]
],
"1": [
Expand All @@ -114,7 +114,7 @@
"id": "test",
"single_end": false
},
"test.vcf.gz.tbi:md5,248648ca03f5fda904ebbef8821e0e37"
"test.vcf.gz.tbi:md5,efb861c33cf51739a4ae13a2e81126b6"
]
],
"2": [
Expand All @@ -123,7 +123,7 @@
"id": "test",
"single_end": false
},
"test.g.vcf.gz:md5,89b2e47883a65bb9cae8f173e782bb17"
"test.g.vcf.gz:md5,71bf2757abd13abed78479887f9de8f6"
]
],
"3": [
Expand All @@ -132,14 +132,14 @@
"id": "test",
"single_end": false
},
"test.g.vcf.gz.tbi:md5,1680c67fe988bc1d8220fbb4127c2c18"
"test.g.vcf.gz.tbi:md5,90732f1ea2188c12fc4dab62da039f63"
]
],
"4": [
[
"DEEPVARIANT_POSTPROCESSVARIANTS",
"deepvariant",
"1.9.0"
"1.10.0"
]
],
"gvcf": [
Expand All @@ -148,7 +148,7 @@
"id": "test",
"single_end": false
},
"test.g.vcf.gz:md5,89b2e47883a65bb9cae8f173e782bb17"
"test.g.vcf.gz:md5,71bf2757abd13abed78479887f9de8f6"
]
],
"gvcf_index": [
Expand All @@ -157,7 +157,7 @@
"id": "test",
"single_end": false
},
"test.g.vcf.gz.tbi:md5,1680c67fe988bc1d8220fbb4127c2c18"
"test.g.vcf.gz.tbi:md5,90732f1ea2188c12fc4dab62da039f63"
]
],
"vcf": [
Expand All @@ -166,7 +166,7 @@
"id": "test",
"single_end": false
},
"test.vcf.gz:md5,707212230030c8c3efbe5c2e0428da03"
"test.vcf.gz:md5,d6ec6971b53fc10bf9ed23ddf6f544c1"
]
],
"vcf_index": [
Expand All @@ -175,14 +175,14 @@
"id": "test",
"single_end": false
},
"test.vcf.gz.tbi:md5,248648ca03f5fda904ebbef8821e0e37"
"test.vcf.gz.tbi:md5,efb861c33cf51739a4ae13a2e81126b6"
]
],
"versions_deepvariant": [
[
"DEEPVARIANT_POSTPROCESSVARIANTS",
"deepvariant",
"1.9.0"
"1.10.0"
]
]
}
Expand All @@ -191,6 +191,6 @@
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-02-02T17:19:32.037352523"
"timestamp": "2026-05-22T13:07:18.932165"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/deepvariant/postprocessvariants/tests/nextflow.config
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Expand Up @@ -5,6 +5,6 @@ process {
}
process {
withName: "DEEPVARIANT_MAKEEXAMPLES" {
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"'
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"'
}
}
6 changes: 5 additions & 1 deletion modules/nf-core/deepvariant/rundeepvariant/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,9 @@ process DEEPVARIANT_RUNDEEPVARIANT {
def par_regions = par_bed ? "--par_regions_bed=${par_bed}" : ""

"""
export MPLCONFIGDIR=\$PWD/.matplotlib
mkdir -p \$MPLCONFIGDIR
Comment thread
jonasscheid marked this conversation as resolved.

/opt/deepvariant/bin/run_deepvariant \\
--ref=${fasta} \\
--reads=${input} \\
Expand All @@ -59,5 +62,6 @@ process DEEPVARIANT_RUNDEEPVARIANT {
echo "stub" | gzip > ${prefix}.vcf.gz
echo "stub" | gzip > ${prefix}.vcf.gz.tbi
echo "stub" | gzip > ${prefix}.g.vcf.gz
echo "stub" | gzip > ${prefix}.g.vcf.gz.tbi """
echo "stub" | gzip > ${prefix}.g.vcf.gz.tbi
"""
}
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