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CaroAMNCaroAMN
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Merge pull request #56 from CaroAMN/dev
update ara subworkflow
2 parents 55e2f02 + bb5777a commit ddf60c1

5 files changed

Lines changed: 70 additions & 77 deletions

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‎conf/modules.config‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -91,7 +91,7 @@ process {
9191
publishDir = [
9292
path: { "${params.outdir}/numorph_resample/" },
9393
mode: params.publish_dir_mode,
94-
pattern: 'results/**/*',
94+
pattern: 'results/*',
9595
saveAs: { filename ->
9696
if (filename.equals('versions.yml')) {
9797
null
@@ -105,7 +105,7 @@ process {
105105
publishDir = [
106106
path: { "${params.outdir}/numorphregister/" },
107107
mode: params.publish_dir_mode,
108-
pattern: 'results/**/*',
108+
pattern: 'results/*',
109109
saveAs: { filename ->
110110
if (filename.equals('versions.yml')) {
111111
null

‎modules/local/numorphregister/main.nf‎

Lines changed: 6 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -2,17 +2,17 @@ process NUMORPHREGISTER {
22
tag "$meta.id"
33
label 'process_high_long'
44

5-
container "nf-core/numorph_analyze:1.0.1"
5+
container "nf-core/numorph_analyze:1.0.0"
66

77
input:
88
tuple val(meta), path(resampled_directory), path(parameter_file)
99

1010
output:
11-
path "results/*results.mat" , emit: res_mat
12-
path "results/variables/*" , emit: variables
13-
path "results/NM_variables.mat" , emit: NM_variables
14-
path "results/registered/*" , emit: registered
15-
path "versions.yml" , emit: versions
11+
tuple val(meta), path("results/registered/") , emit: registered
12+
tuple val(meta), path("results/variables/") , emit: variables
13+
tuple val(meta), path("results/NM_variables.mat") , emit: NM_variables
14+
15+
tuple val("${task.process}"), val('numorphregister'), val('1.0.0'), emit: versions_numorph_analyze, topic: versions
1616

1717

1818
when:
@@ -37,11 +37,6 @@ process NUMORPHREGISTER {
3737
3838
numorph_analyze 'input_dir' \$resampled_directory 'output_dir' \$results_dir 'parameter_file' \$parameter_file 'sample_name' ${prefix} 'stage' 'register' 'NM_variables' '' 'use_processed_images' 'resampled'
3939
40-
41-
cat <<-END_VERSIONS > versions.yml
42-
"${task.process}":
43-
numorphregister: 1.0
44-
END_VERSIONS
4540
"""
4641

4742
stub:
@@ -55,12 +50,7 @@ process NUMORPHREGISTER {
5550
touch results/variables/reg_params.mat
5651
touch results/variables/${prefix}_mask.mat
5752
touch results/NM_variables.mat
58-
touch results/${prefix}_results.mat
5953
touch results/registered/${prefix}_registered.tif
6054
61-
cat <<-END_VERSIONS > versions.yml
62-
"${task.process}":
63-
numorphregister: 1.0
64-
END_VERSIONS
6555
"""
6656
}

‎subworkflows/local/araregistration/main.nf‎

Lines changed: 10 additions & 23 deletions
Original file line numberDiff line numberDiff line change
@@ -25,34 +25,21 @@ workflow ARAREGISTRATION {
2525

2626
NUMORPHREGISTER (resampled_data)
2727

28-
ch_versions = ch_versions.mix(NUMORPHREGISTER.out.versions)
29-
def reg_output = NUMORPHREGISTER.out
30-
31-
def registration_files = reg_output.variables.flatten()
32-
33-
sample_meta.combine(registration_files)
34-
.mix (
35-
sample_meta.combine(reg_output.res_mat),
36-
sample_meta.combine(reg_output.NM_variables)
37-
)
38-
.set {mat_files_reg}
28+
def mat_files = NUMORPHREGISTER.out.variables
29+
.flatMap { meta, variables_dir ->
30+
variables_dir.listFiles()
31+
.findAll { it.name.endsWith('.mat') }
32+
.collect { matfile -> [meta, matfile] }
33+
}
34+
.mix(NUMORPHREGISTER.out.NM_variables)
3935

40-
MAT2JSON (mat_files_reg, "registration")
41-
ch_versions = ch_versions.mix(MAT2JSON.out.versions)
36+
MAT2JSON (mat_files, "registration")
4237

43-
softwareVersionsToYAML(ch_versions)
44-
.collectFile(
45-
storeDir: "${params.outdir}/pipeline_info",
46-
name: 'nf_core_' + 'lsmquant_software_' + 'mqc_' + 'versions.yml',
47-
sort: true,
48-
newLine: true
49-
).set { ch_collated_versions }
5038

5139
emit:
5240

53-
res_mat = NUMORPHREGISTER.out.res_mat
5441
variables = NUMORPHREGISTER.out.variables // channel: variables
5542
registered = NUMORPHREGISTER.out.registered // channel: registered
56-
NM_variables = NUMORPHREGISTER.out.NM_variables // channel: NM_variables
57-
versions = ch_collated_versions // channel: [ versions.yml ]
43+
NM_variable = NUMORPHREGISTER.out.NM_variables // channel: NM_variables
44+
5845
}

‎subworkflows/local/araregistration/tests/main.nf.test‎

Lines changed: 0 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -17,21 +17,6 @@ nextflow_workflow {
1717
test("ARA registration stub test") {
1818

1919
options '-stub'
20-
setup {
21-
run ("NUMORPHINTENSITY") {
22-
script "../../../../modules/local/numorphintensity/main.nf"
23-
options '-stub'
24-
process {
25-
"""
26-
input[0] = Channel.fromList([
27-
tuple([ id:'TEST1'],
28-
file('https://zenodo.org/records/14916478/files/ctip2_topro.zip'),
29-
file(params.pipelines_testdata_base_path + '/test_data/parameterfiles/params_TEST1_lsmquant.csv'))
30-
])
31-
"""
32-
}
33-
}
34-
}
3520

3621
when {
3722
workflow {
@@ -41,7 +26,6 @@ nextflow_workflow {
4126
file('https://zenodo.org/records/14916478/files/ctip2_topro.zip'),
4227
file(params.pipelines_testdata_base_path + '/test_data/parameterfiles/params_TEST1_lsmquant.csv'))
4328
])
44-
input[1] = NUMORPHINTENSITY.out.NM_variables
4529
"""
4630
}
4731
}

‎subworkflows/local/araregistration/tests/main.nf.test.snap‎

Lines changed: 52 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -3,37 +3,69 @@
33
"content": [
44
{
55
"0": [
6-
"TEST1_mask.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
6+
[
7+
{
8+
"id": "TEST1"
9+
},
10+
[
11+
"TEST1_mask.mat:md5,d41d8cd98f00b204e9800998ecf8427e",
12+
"reg_params.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
13+
]
14+
]
715
],
816
"1": [
9-
"TEST1_registered.tif:md5,d41d8cd98f00b204e9800998ecf8427e"
17+
[
18+
{
19+
"id": "TEST1"
20+
},
21+
[
22+
"TEST1_registered.tif:md5,d41d8cd98f00b204e9800998ecf8427e"
23+
]
24+
]
1025
],
1126
"2": [
12-
"NM_variables.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
27+
[
28+
{
29+
"id": "TEST1"
30+
},
31+
"NM_variables.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
32+
]
1333
],
14-
"3": [
15-
"versions.yml:md5,2139e73f27b3197eed0d8d821f002fc8",
16-
"versions.yml:md5,e131f0dbfdba4ab1ac28d4f59f91fc84"
17-
],
18-
"NM_variables": [
19-
"NM_variables.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
20-
],
21-
"reg_mask": [
22-
"TEST1_mask.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
34+
"NM_variable": [
35+
[
36+
{
37+
"id": "TEST1"
38+
},
39+
"NM_variables.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
40+
]
2341
],
2442
"registered": [
25-
"TEST1_registered.tif:md5,d41d8cd98f00b204e9800998ecf8427e"
43+
[
44+
{
45+
"id": "TEST1"
46+
},
47+
[
48+
"TEST1_registered.tif:md5,d41d8cd98f00b204e9800998ecf8427e"
49+
]
50+
]
2651
],
27-
"versions": [
28-
"versions.yml:md5,2139e73f27b3197eed0d8d821f002fc8",
29-
"versions.yml:md5,e131f0dbfdba4ab1ac28d4f59f91fc84"
52+
"variables": [
53+
[
54+
{
55+
"id": "TEST1"
56+
},
57+
[
58+
"TEST1_mask.mat:md5,d41d8cd98f00b204e9800998ecf8427e",
59+
"reg_params.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
60+
]
61+
]
3062
]
3163
}
3264
],
65+
"timestamp": "2026-03-23T11:13:30.487550704",
3366
"meta": {
34-
"nf-test": "0.9.2",
35-
"nextflow": "25.04.6"
36-
},
37-
"timestamp": "2025-08-26T13:41:44.200641791"
67+
"nf-test": "0.9.4",
68+
"nextflow": "25.10.3"
69+
}
3870
}
3971
}

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