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Update Genome Nexus annotation module args #249

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Update Genome Nexus annotation module args #249

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11a5b89
Update Genome Nexus annotation module args
johnoooh Jun 9, 2026
4137414
Update Genome Nexus annotation snapshot
johnoooh Jun 10, 2026
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13 changes: 9 additions & 4 deletions modules/msk/genomenexus/annotationpipeline/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -20,9 +20,15 @@ process GENOMENEXUS_ANNOTATIONPIPELINE {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def xms = Math.max(256, (task.memory.toMega() / 4) as int)
def xmx = Math.max(1, task.memory.toGiga() as int)

"""
java -Xms${task.memory.toMega()/4}m -Xmx${task.memory.toGiga()}g -jar /genome-nexus-annotation-pipeline/annotationPipeline/target/annotationPipeline.jar --filename ${input_maf} --output-filename ${meta.id}-annotated.maf
java -Xms${xms}m -Xmx${xmx}g \\
-jar /genome-nexus-annotation-pipeline/annotationPipeline/target/annotationPipeline.jar \\
--filename ${input_maf} \\
--output-filename ${prefix}-annotated.maf \\
${args}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand All @@ -31,15 +37,14 @@ process GENOMENEXUS_ANNOTATIONPIPELINE {
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"

"""
touch ${meta.id}-annotated.maf
touch ${prefix}-annotated.maf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
genomenexus: 'annotation pipeline version 1.0.5
genomenexus: 'annotationpipeline version 1.0.5'
END_VERSIONS
"""
}
8 changes: 4 additions & 4 deletions modules/msk/genomenexus/annotationpipeline/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -41,24 +41,24 @@ nextflow_process {

test("test normal - stub") {

tag "stub"
options "-stub"

when {
process {
"""


input[0] = [
[ id:'test',case_id:'sample1',control_id:'sample2'], // meta map
file(params.test_data_mskcc['genome_nexus']['sample2_sample1_annotated_maf'], checkIfExists: true)
file('dummy.maf', checkIfExists: false)
]
"""
}
}

then {
assertAll(
{ assert process.success }
{ assert process.success },
{ assert snapshot(process.out).match() }

)
}
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47 changes: 44 additions & 3 deletions modules/msk/genomenexus/annotationpipeline/tests/main.nf.test.snap
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Expand Up @@ -9,7 +9,7 @@
"case_id": "sample1",
"control_id": "sample2"
},
"test-annotated.maf:md5,4547e768939e82f6d1f44e1c64b64c3a"
"test-annotated.maf:md5,a8b47024c381dc8f2e5b2c0da0b24029"
]
],
"1": [
Expand All @@ -22,14 +22,55 @@
"case_id": "sample1",
"control_id": "sample2"
},
"test-annotated.maf:md5,4547e768939e82f6d1f44e1c64b64c3a"
"test-annotated.maf:md5,a8b47024c381dc8f2e5b2c0da0b24029"
]
],
"versions": [
"versions.yml:md5,3eec02db5105ee47caf6ea6efb53f12c"
]
}
],
"timestamp": "2024-11-26T16:50:32.331962"
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.10.3"
},
"timestamp": "2026-06-10T11:03:28.679902"
},
"test normal - stub": {
"content": [
{
"0": [
[
{
"id": "test",
"case_id": "sample1",
"control_id": "sample2"
},
"test-annotated.maf:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"versions.yml:md5,3eec02db5105ee47caf6ea6efb53f12c"
],
"annotated_maf": [
[
{
"id": "test",
"case_id": "sample1",
"control_id": "sample2"
},
"test-annotated.maf:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,3eec02db5105ee47caf6ea6efb53f12c"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.10.3"
},
"timestamp": "2026-06-09T17:03:25.918345"
}
}
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