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CaroAMNCaroAMN
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‎modules/local/numorph3dunet/main.nf‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -5,6 +5,7 @@ process NUMORPH3DUNET {
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container "carolinschwitalla/numorph-3dunet:latest"
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containerOptions '--gpus all'
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input:
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tuple val(meta), path(input_dir), path(parameter_file)

‎modules/local/numorph3dunet/tests/main.nf.test‎

Lines changed: 80 additions & 46 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,3 @@
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// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
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// nf-core modules test numorph3dunet
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nextflow_process {
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name "Test Process NUMORPH3DUNET"
@@ -9,65 +7,101 @@ nextflow_process {
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tag "modules"
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tag "modules_"
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tag "numorph3dunet"
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tag "gpu"
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// TODO nf-core: Change the test name preferably indicating the test-data and file-format used
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test("sarscov2 - bam") {
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// TODO nf-core: If you are created a test for a chained module
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// (the module requires running more than one process to generate the required output)
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// add the 'setup' method here.
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// You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules).
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when {
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process {
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"""
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// TODO nf-core: define inputs of the process here. Example:
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input[0] = [
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[ id:'test', single_end:false ], // meta map
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file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
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]
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test("Numorph3DUnet test - tif") {
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setup {
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run ("UNZIP") {
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script "../../../nf-core/unzip/main.nf"
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process {
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"""
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input[0] = Channel.fromList([
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tuple([ id:'TEST1'],
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file('https://zenodo.org/records/14916478/files/ctip2_topro.zip'))
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])
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"""
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}
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}
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run ("NUMORPHINTENSITY") {
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script "../../numorphintensity/main.nf"
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process {
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"""
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input[0] = UNZIP.out.unzipped_archive.map { meta, unzipped_archive ->
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tuple(
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meta,
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unzipped_archive,
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file(params.pipelines_testdata_base_path + '/test_data/parameterfiles/params_TEST1_lsmquant.csv'))
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}
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"""
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}
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}
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run ("NUMORPHALIGN") {
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script "../../numorphalign/main.nf"
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process {
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"""
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input[0] = UNZIP.out.unzipped_archive.map { meta, unzipped_archive ->
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tuple(
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meta,
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unzipped_archive,
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file(params.pipelines_testdata_base_path + '/test_data/parameterfiles/params_TEST1_lsmquant.csv'))
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} //
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input[1] = NUMORPHINTENSITY.out.adj_params_mat
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input[2] = NUMORPHINTENSITY.out.path_table_mat
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input[3] = NUMORPHINTENSITY.out.thresholds_mat
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input[4] = NUMORPHINTENSITY.out.NM_variables
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"""
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}
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}
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run ("NUMORPHSTITCH") {
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script "../../numorphstitch/main.nf"
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process {
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"""
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input[0] = UNZIP.out.unzipped_archive.map { meta, unzipped_archive ->
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tuple(
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meta,
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unzipped_archive,
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file(params.pipelines_testdata_base_path + '/test_data/parameterfiles/params_TEST1_lsmquant.csv'))
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}
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input[1] = NUMORPHALIGN.out.alignment_table_mat
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input[2] = NUMORPHALIGN.out.z_displacement_align_mat
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input[3] = NUMORPHALIGN.out.path_table_mat
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input[4] = NUMORPHINTENSITY.out.thresholds_mat
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input[5] = NUMORPHINTENSITY.out.adj_params_mat
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input[6] = NUMORPHALIGN.out.NM_variables
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"""
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}
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(process.out).match() }
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//TODO nf-core: Add all required assertions to verify the test output.
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// See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples.
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)
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}
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}
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// TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
46-
test("sarscov2 - bam - stub") {
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options "-stub"
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when {
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params {
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outdir = "$workDir/output"
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}
5179
process {
5280
"""
53-
// TODO nf-core: define inputs of the process here. Example:
54-
55-
input[0] = [
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[ id:'test', single_end:false ], // meta map
57-
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
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]
81+
input[0] = NUMORPHSTITCH.out.stitched.map { meta, stitched ->
82+
tuple(
83+
meta,
84+
stitched,
85+
file(params.pipelines_testdata_base_path + '/test_data/parameterfiles/params_TEST1_lsmquant.csv'))
86+
}
87+
input[1] = Channel.fromPath('/home/schwitalla/Documents/numorph_3dunet/src/numorph_3dunet/models/075_121_model.h5')
88+
input[2] = Channel.from(1) // number of channels
5989
"""
6090
}
6191
}
6292

6393
then {
94+
def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
95+
assert workflow.success
6496
assertAll(
65-
{ assert process.success },
66-
{ assert snapshot(process.out).match() }
67-
//TODO nf-core: Add all required assertions to verify the test output.
97+
{ assert snapshot(
98+
// Number of successful tasks
99+
workflow.trace.succeeded().size(),
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// All stable path name, with a relative path
101+
stable_name.isEmpty() ? 'No stable paths' : stable_name
102+
).match()}
68103
)
69104
}
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}
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}

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