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Migrate bundle/recognize module to scilpy 2.0.0 + nf-test #134

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Apr 29, 2024
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Migrate bundle/recognize module to scilpy 2.0.0 + nf-test #134

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3487d59
[WIP] Migrate bundle/recognize module to scilpy 2.0.0 + nf-test
gagnonanthony Apr 24, 2024
701a6d9
[FIX] prettier + editorconfig
gagnonanthony Apr 24, 2024
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7 changes: 7 additions & 0 deletions modules/nf-scil/bundle/recognize/environment.yml
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---
name: "bundle_recognize"
channels:
- Docker
- Apptainer
dependencies:
- "Scilpy"
18 changes: 9 additions & 9 deletions modules/nf-scil/bundle/recognize/main.nf
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Expand Up @@ -3,8 +3,8 @@ process BUNDLE_RECOGNIZE {
label 'process_single'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://scil.usherbrooke.ca/containers/scilus_1.6.0.sif':
'scilus/scilus:1.6.0' }"
'https://scil.usherbrooke.ca/containers/scilus_2.0.0.sif':
'scilus/scilus:2.0.0' }"

input:
tuple val(meta), path(tractograms), path(transform), path(config), path(directory)
Expand All @@ -26,33 +26,33 @@ process BUNDLE_RECOGNIZE {
def outlier_alpha = task.ext.outlier_alpha ? "--alpha " + task.ext.outlier_alpha : ""
"""
mkdir recobundles/
scil_recognize_multi_bundles.py ${tractograms} ${config} ${directory}/ ${transform} --inverse --out_dir recobundles/ \
--log_level DEBUG $minimal_vote_ratio $seed $rbx_processes
scil_tractogram_segment_bundles.py ${tractograms} ${config} ${directory}/ ${transform} --inverse --out_dir recobundles/ \
-v DEBUG $minimal_vote_ratio $seed $rbx_processes

for bundle_file in recobundles/*.trk; do
bname=\$(basename \${bundle_file} .trk)
out_cleaned=${prefix}__\${bname}_cleaned.trk
scil_outlier_rejection.py \${bundle_file} "\${out_cleaned}" ${outlier_alpha}
scil_bundle_reject_outliers.py \${bundle_file} "\${out_cleaned}" ${outlier_alpha}
done

cat <<-END_VERSIONS > versions.yml
"${task.process}":
scilpy: 1.6.0
scilpy: 2.0.0
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
scil_recognize_multi_bundles.py -h
scil_outlier_rejection.py -h
scil_tractogram_segment_bundles.py -h
scil_bundle_reject_outliers.py -h

# dummy output for single bundle
touch ${prefix}__AF_L_cleaned.trk

cat <<-END_VERSIONS > versions.yml
"${task.process}":
scilpy: 1.6.0
scilpy: 2.0.0
END_VERSIONS
"""
}
85 changes: 85 additions & 0 deletions modules/nf-scil/bundle/recognize/tests/main.nf.test
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nextflow_process {

name "Test Process BUNDLE_RECOGNIZE"
script "../main.nf"
process "BUNDLE_RECOGNIZE"

tag "modules"
tag "modules_nfcore"
tag "bundle"
tag "bundle/recognize"

tag "subworkflows"
tag "subworkflows/load_test_data"

setup {
run("LOAD_TEST_DATA", alias: "LOAD_DATA") {
script "../../../../../subworkflows/nf-scil/load_test_data/main.nf"
process {
"""
input[0] = Channel.from( [ "bundles.zip" ] )
input[1] = "test.load-test-data"
"""
}
}
}

test("bundle - recognize - base") {

config "./nextflow.config"

when {
process {
"""
input[0] = LOAD_DATA.out.test_data_directory.map{
test_data_directory -> [
[ id:'test', single_end:false ], // meta map
file("\${test_data_directory}/bundle_all_1mm.trk"),
file("\${test_data_directory}/affine.txt"),
file("\${test_data_directory}/config.json"),
file("\${test_data_directory}/fibercup_atlas/")
]
}
"""
}
}

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

}

test("bundle - recognize - params") {

config "./nextflow_params.config"

when {
process {
"""
input[0] = LOAD_DATA.out.test_data_directory.map{
test_data_directory -> [
[ id:'test', single_end:false ], // meta map
file("\${test_data_directory}/bundle_all_1mm.trk"),
file("\${test_data_directory}/affine.txt"),
file("\${test_data_directory}/config.json"),
file("\${test_data_directory}/fibercup_atlas/")
]
}
"""
}
}

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

}

}
96 changes: 96 additions & 0 deletions modules/nf-scil/bundle/recognize/tests/main.nf.test.snap
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{
"bundle - recognize - params": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
[
"test__bundle_1_cleaned.trk:md5,4f5cb88d05f175d6b55509d0ad307ab3",
"test__bundle_2_cleaned.trk:md5,58b4c1381603d72ad6e72cc705b4606e",
"test__bundle_3_cleaned.trk:md5,8f24a8c534b6e2386bcc755bd8f0c4b9",
"test__bundle_4_cleaned.trk:md5,eafac0796051d6ada4bfc5a5c576c536",
"test__bundle_5_cleaned.trk:md5,0d512bcaaf49325415a1f4860a167f5e"
]
]
],
"1": [
"versions.yml:md5,33bf1f04d87c84bb617311a892ba882a"
],
"bundles": [
[
{
"id": "test",
"single_end": false
},
[
"test__bundle_1_cleaned.trk:md5,4f5cb88d05f175d6b55509d0ad307ab3",
"test__bundle_2_cleaned.trk:md5,58b4c1381603d72ad6e72cc705b4606e",
"test__bundle_3_cleaned.trk:md5,8f24a8c534b6e2386bcc755bd8f0c4b9",
"test__bundle_4_cleaned.trk:md5,eafac0796051d6ada4bfc5a5c576c536",
"test__bundle_5_cleaned.trk:md5,0d512bcaaf49325415a1f4860a167f5e"
]
]
],
"versions": [
"versions.yml:md5,33bf1f04d87c84bb617311a892ba882a"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-04-24T10:58:28.42142"
},
"bundle - recognize - base": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
[
"test__bundle_1_cleaned.trk:md5,6a5c47dccc9f51087572a8de006183ae",
"test__bundle_2_cleaned.trk:md5,08e2bd3fe0432d4dd58b7db771c8080d",
"test__bundle_3_cleaned.trk:md5,313c4401e7771a966c26be3f73ea7730",
"test__bundle_4_cleaned.trk:md5,b2e8e5a6b9077d6a36552b6bfa579de4",
"test__bundle_5_cleaned.trk:md5,3b975ace291d6fd4fd434ce37cc2263a"
]
]
],
"1": [
"versions.yml:md5,33bf1f04d87c84bb617311a892ba882a"
],
"bundles": [
[
{
"id": "test",
"single_end": false
},
[
"test__bundle_1_cleaned.trk:md5,6a5c47dccc9f51087572a8de006183ae",
"test__bundle_2_cleaned.trk:md5,08e2bd3fe0432d4dd58b7db771c8080d",
"test__bundle_3_cleaned.trk:md5,313c4401e7771a966c26be3f73ea7730",
"test__bundle_4_cleaned.trk:md5,b2e8e5a6b9077d6a36552b6bfa579de4",
"test__bundle_5_cleaned.trk:md5,3b975ace291d6fd4fd434ce37cc2263a"
]
]
],
"versions": [
"versions.yml:md5,33bf1f04d87c84bb617311a892ba882a"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-04-24T10:55:40.819871"
}
}
5 changes: 5 additions & 0 deletions modules/nf-scil/bundle/recognize/tests/nextflow.config
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process {
withName: "BUNDLE_RECOGNIZE" {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}
}
5 changes: 1 addition & 4 deletions .../nf-scil/bundle/recognize/nextflow.config → ...le/recognize/tests/nextflow_params.config
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@@ -1,11 +1,8 @@
process {
withName: "BUNDLE_RECOGNIZE" {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}

withName: "BUNDLE_RECOGNIZE_PARAMS" {
ext.minimal_vote_ratio = 0.6
ext.seed = 1234
ext.outlier_alpha = 0.4
}
}
}
2 changes: 2 additions & 0 deletions modules/nf-scil/bundle/recognize/tests/tags.yml
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@@ -0,0 +1,2 @@
bundle/recognize:
- "modules/nf-scil/bundle/recognize/**"
3 changes: 0 additions & 3 deletions tests/config/pytest_modules.yml
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Expand Up @@ -7,9 +7,6 @@ betcrop/cropvolume:
betcrop/fslbetcrop:
- modules/nf-scil/betcrop/fslbetcrop/**
- tests/modules/nf-scil/betcrop/fslbetcrop/**
bundle/recognize:
- modules/nf-scil/bundle/recognize/**
- tests/modules/nf-scil/bundle/recognize/**
denoising/mppca:
- modules/nf-scil/denoising/mppca/**
- tests/modules/nf-scil/denoising/mppca/**
Expand Down
44 changes: 0 additions & 44 deletions tests/modules/nf-scil/bundle/recognize/main.nf
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35 changes: 0 additions & 35 deletions tests/modules/nf-scil/bundle/recognize/test.yml
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