8000 nf-test for local execute_clustering subworkflow by vagkaratzas · Pull Request #53 · nf-core/proteinfamilies · GitHub
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nf-test for local execute_clustering subworkflow #53

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Merged
merged 6 commits into from
Mar 25, 2025
Merged

nf-test for local execute_clustering subworkflow #53

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743f7d3
nf-test for local execute_clustering subworkflow, passing the cluster…
vagkaratzas Mar 25, 2025
0dd17e9
changelog updated
vagkaratzas Mar 25, 2025
88936a2
testDir added
vagkaratzas Mar 25, 2025
275f970
Merge branch 'dev' into nf-test-execute_clustering
vagkaratzas Mar 25, 2025
5bd4844
Merge branch 'dev' into nf-test-execute_clustering
vagkaratzas Mar 25, 2025
aae01e4
explicitly state linclust as the alternate option, anything else is c…
vagkaratzas Mar 25, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### `Added`

- [#54](https://github.com/nf-core/proteinfamilies/pull/54) - Added nf-test for local subworkflow `ALIGN_SEQUENCES`
- [#53](https://github.com/nf-core/proteinfamilies/pull/53) - Added nf-test for local subworkflow `EXECUTE_CLUSTERING`
- [#51](https://github.com/nf-core/proteinfamilies/pull/51) - Added nf-test and `meta.yml` file for local module `CALCULATE_CLUSTER_DISTRIBUTION`
- [#34](https://github.com/nf-core/proteinfamilies/pull/34) - Added the `EXTRACT_UNIQUE_CLUSTER_REPS` module, that calculates initial `MMseqs` clustering metadata, for each sample, to print with `MultiQC` (Id,Cluster Size,Number of Clusters)

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7 changes: 4 additions & 3 deletions subworkflows/local/execute_clustering/main.nf
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Expand Up @@ -9,7 +9,8 @@ include { MMSEQS_CREATETSV } from '../../../modules/nf-core/mmseqs/createtsv/mai

workflow EXECUTE_CLUSTERING {
take:
sequences // tuple val(meta), path(fasta)
sequences // tuple val(meta), path(fasta)
clustering_tool // string: mmseqs clustering algorithm

main:
ch_versions = Channel.empty()
Expand All @@ -18,10 +19,10 @@ workflow EXECUTE_CLUSTERING {
MMSEQS_CREATEDB( sequences )
ch_versions = ch_versions.mix( MMSEQS_CREATEDB.out.versions )

if (params.clustering_tool == 'cluster') {
if (clustering_tool == 'cluster') {
cluster_res = MMSEQS_CLUSTER( MMSEQS_CREATEDB.out.db )
ch_versions = ch_versions.mix( MMSEQS_CLUSTER.out.versions )
} else { // fallback: linclust
} else if (clustering_tool == 'linclust') {
cluster_res = MMSEQS_LINCLUST( MMSEQS_CREATEDB.out.db )
ch_versions = ch_versions.mix( MMSEQS_LINCLUST.out.versions )
}
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115 changes: 115 additions & 0 deletions subworkflows/local/execute_clustering/tests/main.nf.test
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@@ -0,0 +1,115 @@
nextflow_workflow {

name "Test Subworkflow EXECUTE_CLUSTERING"
script "../main.nf"
workflow "EXECUTE_CLUSTERING"

test("fasta - linclust") {

when {
workflow {
"""
clustering_tool = 'linclust'

input[0] = Channel.of([
[ id: 'test_linclust' ], // meta map
file(params.pipelines_testdata_base_path + 'proteinfamilies/test_data/mgnifams_input_small.fa', checkIfExists: true)
])
input[1] = clustering_tool
"""
}
}

then {
def lines = path(workflow.out.clusters[0][1]).readLines()
assertAll(
{ assert workflow.success},
{ assert snapshot(
file(workflow.out.clusters[0][1]).name,
lines.size(),
workflow.out.versions).match() }
)
}
}

test("fasta - cluster") {

when {
workflow {
"""
clustering_tool = 'cluster'

input[0] = Channel.of([
[ id: 'test_cluster' ], // meta map
file(params.pipelines_testdata_base_path + 'proteinfamilies/test_data/mgnifams_input_small.fa', checkIfExists: true)
])
input[1] = clustering_tool
"""
}
}

then {
def lines = path(workflow.out.clusters[0][1]).readLines()
assertAll(
{ assert workflow.success},
{ assert snapshot(
file(workflow.out.clusters[0][1]).name,
lines.size(),
workflow.out.versions).match() }
)
}
}

test("fasta - linclust - stub") {

options "-stub"

when {
workflow {
"""
clustering_tool = 'linclust'

input[0] = Channel.of([
[ id: 'test_linclust_stub' ], // meta map
file(params.pipelines_testdata_base_path + 'proteinfamilies/test_data/mgnifams_input_small.fa', checkIfExists: true)
])
input[1] = clustering_tool
"""
}
}

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

test("fasta - cluster - stub") {

options "-stub"

when {
workflow {
"""
clustering_tool = 'cluster'

input[0] = Channel.of([
[ id: 'test_cluster_stub' ], // meta map
file(params.pipelines_testdata_base_path + 'proteinfamilies/test_data/mgnifams_input_small.fa', checkIfExists: true)
])
input[1] = clustering_tool
"""
}
}

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

}
140 changes: 140 additions & 0 deletions subworkflows/local/execute_clustering/tests/main.nf.test.snap
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@@ -0,0 +1,140 @@
{
"fasta - cluster": {
"content": [
"test_cluster.tsv",
50000,
[
"versions.yml:md5,3312bc6e1fa1b06e4a8ac2603deba2a4",
"versions.yml:md5,40b242fe8ca427ffe7cd860dc5b9d7fc",
"versions.yml:md5,9d06e5efe2356113924a205c58f0b42f"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-03-25T08:35:58.03861131"
},
"fasta - linclust - stub": {
"content": [
{
"0": [
"versions.yml:md5,3312bc6e1fa1b06e4a8ac2603deba2a4",
"versions.yml:md5,9d06e5efe2356113924a205c58f0b42f",
"versions.yml:md5,c3f8381c74eb9f0a2d549f273ba89595"
],
"1": [
[
{
"id": "test_linclust_stub"
},
"/nf-core/test-datasets/proteinfamilies/test_data/mgnifams_input_small.fa"
]
],
"2": [
[
{
"id": "test_linclust_stub"
},
"test_linclust_stub.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"clusters": [
[
{
"id": "test_linclust_stub"
},
"test_linclust_stub.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"seqs": [
[
{
"id": "test_linclust_stub"
},
"/nf-core/test-datasets/proteinfamilies/test_data/mgnifams_input_small.fa"
]
],
"versions": [
"versions.yml:md5,3312bc6e1fa1b06e4a8ac2603deba2a4",
"versions.yml:md5,9d06e5efe2356113924a205c58f0b42f",
"versions.yml:md5,c3f8381c74eb9f0a2d549f273ba89595"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-03-25T08:36:09.660114354"
},
"fasta - linclust": {
"content": [
"test_linclust.tsv",
50000,
[
"versions.yml:md5,3312bc6e1fa1b06e4a8ac2603deba2a4",
"versions.yml:md5,9d06e5efe2356113924a205c58f0b42f",
"versions.yml:md5,c3f8381c74eb9f0a2d549f273ba89595"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-03-25T08:35:24.00287769"
},
"fasta - cluster - stub": {
"content": [
{
"0": [
"versions.yml:md5,3312bc6e1fa1b06e4a8ac2603deba2a4",
"versions.yml:md5,40b242fe8ca427ffe7cd860dc5b9d7fc",
"versions.yml:md5,9d06e5efe2356113924a205c58f0b42f"
],
"1": [
[
{
"id": "test_cluster_stub"
},
"/nf-core/test-datasets/proteinfamilies/test_data/mgnifams_input_small.fa"
]
],
"2": [
[
{
"id": "test_cluster_stub"
},
"test_cluster_stub.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"clusters": [
[
{
"id": "test_cluster_stub"
},
"test_cluster_stub.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"seqs": [
[
{
"id": "test_cluster_stub"
},
"/nf-core/test-datasets/proteinfamilies/test_data/mgnifams_input_small.fa"
]
],
"versions": [
"versions.yml:md5,3312bc6e1fa1b06e4a8ac2603deba2a4",
"versions.yml:md5,40b242fe8ca427ffe7cd860dc5b9d7fc",
"versions.yml:md5,9d06e5efe2356113924a205c58f0b42f"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-03-25T08:36:21.001725949"
}
}
2 changes: 1 addition & 1 deletion subworkflows/local/remove_redundancy/main.nf
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Expand Up @@ -76,7 +76,7 @@ workflow REMOVE_REDUNDANCY {
}

if (params.remove_sequence_redundancy) {
EXECUTE_CLUSTERING( fasta )
EXECUTE_CLUSTERING( fasta, params.clustering_tool )
ch_versions = ch_versions.mix( EXECUTE_CLUSTERING.out.versions )

REMOVE_REDUNDANT_SEQS( EXECUTE_CLUSTERING.out.clusters, EXECUTE_CLUSTERING.out.seqs )
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2 changes: 1 addition & 1 deletion subworkflows/local/update_families/main.nf
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Expand Up @@ -101,7 +101,7 @@ workflow UPDATE_FAMILIES {

if (params.remove_sequence_redundancy) {
// Strict clustering to remove redundancy
EXECUTE_CLUSTERING( fasta_ch )
EXECUTE_CLUSTERING( fasta_ch, params.clustering_tool )
ch_versions = ch_versions.mix( EXECUTE_CLUSTERING.out.versions )

REMOVE_REDUNDANT_SEQS( EXECUTE_CLUSTERING.out.clusters, EXECUTE_CLUSTERING.out.seqs )
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1 change: 1 addition & 0 deletions tests/nextflow.config
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@@ -1,3 +1,4 @@
// Impose sensible resource limits for testing
process {
withName: '.*' {
cpus = 2
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2 changes: 1 addition & 1 deletion workflows/proteinfamilies.nf
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Expand Up @@ -80,7 +80,7 @@ workflow PROTEINFAMILIES {

// Creating new families
// Clustering
EXECUTE_CLUSTERING( ch_samplesheet_for_create )
EXECUTE_CLUSTERING( ch_samplesheet_for_create, params.clustering_tool )
ch_versions = ch_versions.mix( EXECUTE_CLUSTERING.out.versions )

CALCULATE_CLUSTER_DISTRIBUTION( EXECUTE_CLUSTERING.out.clusters )
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