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Merged
CaroAMN merged 1 commit into from
Mar 23, 2026
Merged

update ara subworkflow #56

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4 changes: 2 additions & 2 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -91,7 +91,7 @@ process {
publishDir = [
path: { "${params.outdir}/numorph_resample/" },
mode: params.publish_dir_mode,
pattern: 'results/**/*',
pattern: 'results/*',
saveAs: { filename ->
if (filename.equals('versions.yml')) {
null
Expand All @@ -105,7 +105,7 @@ process {
publishDir = [
path: { "${params.outdir}/numorphregister/" },
mode: params.publish_dir_mode,
pattern: 'results/**/*',
pattern: 'results/*',
saveAs: { filename ->
if (filename.equals('versions.yml')) {
null
Expand Down
22 changes: 6 additions & 16 deletions modules/local/numorphregister/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -2,17 +2,17 @@ process NUMORPHREGISTER {
tag "$meta.id"
label 'process_high_long'

container "nf-core/numorph_analyze:1.0.1"
container "nf-core/numorph_analyze:1.0.0"

input:
tuple val(meta), path(resampled_directory), path(parameter_file)

output:
path "results/*results.mat" , emit: res_mat
path "results/variables/*" , emit: variables
path "results/NM_variables.mat" , emit: NM_variables
path "results/registered/*" , emit: registered
path "versions.yml" , emit: versions
tuple val(meta), path("results/registered/") , emit: registered
tuple val(meta), path("results/variables/") , emit: variables
tuple val(meta), path("results/NM_variables.mat") , emit: NM_variables

tuple val("${task.process}"), val('numorphregister'), val('1.0.0'), emit: versions_numorph_analyze, topic: versions


when:
Expand All @@ -37,11 +37,6 @@ process NUMORPHREGISTER {

numorph_analyze 'input_dir' \$resampled_directory 'output_dir' \$results_dir 'parameter_file' \$parameter_file 'sample_name' ${prefix} 'stage' 'register' 'NM_variables' '' 'use_processed_images' 'resampled'


cat <<-END_VERSIONS > versions.yml
"${task.process}":
numorphregister: 1.0
END_VERSIONS
"""

stub:
Expand All @@ -55,12 +50,7 @@ process NUMORPHREGISTER {
touch results/variables/reg_params.mat
touch results/variables/${prefix}_mask.mat
touch results/NM_variables.mat
touch results/${prefix}_results.mat
touch results/registered/${prefix}_registered.tif

cat <<-END_VERSIONS > versions.yml
"${task.process}":
numorphregister: 1.0
END_VERSIONS
"""
}
33 changes: 10 additions & 23 deletions subworkflows/local/araregistration/main.nf
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Expand Up @@ -25,34 +25,21 @@ workflow ARAREGISTRATION {

NUMORPHREGISTER (resampled_data)

ch_versions = ch_versions.mix(NUMORPHREGISTER.out.versions)
def reg_output = NUMORPHREGISTER.out

def registration_files = reg_output.variables.flatten()

sample_meta.combine(registration_files)
.mix (
sample_meta.combine(reg_output.res_mat),
sample_meta.combine(reg_output.NM_variables)
)
.set {mat_files_reg}
def mat_files = NUMORPHREGISTER.out.variables
.flatMap { meta, variables_dir ->
variables_dir.listFiles()
.findAll { it.name.endsWith('.mat') }
.collect { matfile -> [meta, matfile] }
}
.mix(NUMORPHREGISTER.out.NM_variables)

MAT2JSON (mat_files_reg, "registration")
ch_versions = ch_versions.mix(MAT2JSON.out.versions)
MAT2JSON (mat_files, "registration")

softwareVersionsToYAML(ch_versions)
.collectFile(
storeDir: "${params.outdir}/pipeline_info",
name: 'nf_core_' + 'lsmquant_software_' + 'mqc_' + 'versions.yml',
sort: true,
newLine: true
).set { ch_collated_versions }

emit:

res_mat = NUMORPHREGISTER.out.res_mat
variables = NUMORPHREGISTER.out.variables // channel: variables
registered = NUMORPHREGISTER.out.registered // channel: registered
NM_variables = NUMORPHREGISTER.out.NM_variables // channel: NM_variables
versions = ch_collated_versions // channel: [ versions.yml ]
NM_variable = NUMORPHREGISTER.out.NM_variables // channel: NM_variables

}
16 changes: 0 additions & 16 deletions subworkflows/local/araregistration/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -17,21 +17,6 @@ nextflow_workflow {
test("ARA registration stub test") {

options '-stub'
setup {
run ("NUMORPHINTENSITY") {
script "../../../../modules/local/numorphintensity/main.nf"
options '-stub'
process {
"""
input[0] = Channel.fromList([
tuple([ id:'TEST1'],
file('https://zenodo.org/records/14916478/files/ctip2_topro.zip'),
file(params.pipelines_testdata_base_path + '/test_data/parameterfiles/params_TEST1_lsmquant.csv'))
])
"""
}
}
}

when {
workflow {
Expand All @@ -41,7 +26,6 @@ nextflow_workflow {
file('https://zenodo.org/records/14916478/files/ctip2_topro.zip'),
file(params.pipelines_testdata_base_path + '/test_data/parameterfiles/params_TEST1_lsmquant.csv'))
])
input[1] = NUMORPHINTENSITY.out.NM_variables
"""
}
}
Expand Down
72 changes: 52 additions & 20 deletions subworkflows/local/araregistration/tests/main.nf.test.snap
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Expand Up @@ -3,37 +3,69 @@
"content": [
{
"0": [
"TEST1_mask.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
[
{
"id": "TEST1"
},
[
"TEST1_mask.mat:md5,d41d8cd98f00b204e9800998ecf8427e",
"reg_params.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
],
"1": [
"TEST1_registered.tif:md5,d41d8cd98f00b204e9800998ecf8427e"
[
{
"id": "TEST1"
},
[
"TEST1_registered.tif:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
],
"2": [
"NM_variables.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
[
{
"id": "TEST1"
},
"NM_variables.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"3": [
"versions.yml:md5,2139e73f27b3197eed0d8d821f002fc8",
"versions.yml:md5,e131f0dbfdba4ab1ac28d4f59f91fc84"
],
"NM_variables": [
"NM_variables.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"reg_mask": [
"TEST1_mask.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
"NM_variable": [
[
{
"id": "TEST1"
},
"NM_variables.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"registered": [
"TEST1_registered.tif:md5,d41d8cd98f00b204e9800998ecf8427e"
[
{
"id": "TEST1"
},
[
"TEST1_registered.tif:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
],
"versions": [
"versions.yml:md5,2139e73f27b3197eed0d8d821f002fc8",
"versions.yml:md5,e131f0dbfdba4ab1ac28d4f59f91fc84"
"variables": [
[
{
"id": "TEST1"
},
[
"TEST1_mask.mat:md5,d41d8cd98f00b204e9800998ecf8427e",
"reg_params.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
]
}
],
"timestamp": "2026-03-23T11:13:30.487550704",
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
},
"timestamp": "2025-08-26T13:41:44.200641791"
"nf-test": "0.9.4",
"nextflow": "25.10.3"
}
}
}
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