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Address review comments for clustering custom modules
1 parent 3a26119 commit e4877e4

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Lines changed: 87 additions & 87 deletions

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modules/nf-core/custom/cluster_metrics/environment.yml renamed to modules/nf-core/custom/clustermetrics/environment.yml

File renamed without changes.

modules/nf-core/custom/cluster_metrics/main.nf renamed to modules/nf-core/custom/clustermetrics/main.nf

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -32,7 +32,7 @@ process CLUSTER_METRICS {
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def prefix = task.ext.prefix ?: out_prefix ?: "${meta.id}"
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"""
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python3 ${projectDir}/modules/nf-core/custom/cluster_metrics/templates/cluster_metrics.py \\
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python3 ${moduleDir}/templates/cluster_metrics.py \\
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--features ${features} \\
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--clusters ${clusters} \\
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--out-k-sweep ${prefix}_k_sweep.csv \\

modules/nf-core/custom/cluster_metrics/meta.yml renamed to modules/nf-core/custom/clustermetrics/meta.yml

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@@ -1,4 +1,4 @@
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name: "cluster_metrics"
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name: "clustermetrics"
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description: "Computes clustering quality metrics (silhouette, Calinski-Harabasz,
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Davies-Bouldin) and performs k-sweep analysis"
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keywords:

modules/nf-core/custom/cluster_metrics/templates/cluster_metrics.py renamed to modules/nf-core/custom/clustermetrics/templates/cluster_metrics.py

File renamed without changes.

modules/nf-core/custom/cluster_metrics/tests/data/test_clusters.csv renamed to modules/nf-core/custom/clustermetrics/tests/data/test_clusters.csv

File renamed without changes.

modules/nf-core/custom/cluster_metrics/tests/data/test_features.tsv renamed to modules/nf-core/custom/clustermetrics/tests/data/test_features.tsv

File renamed without changes.

modules/nf-core/custom/cluster_metrics/tests/main.nf.test renamed to modules/nf-core/custom/clustermetrics/tests/main.nf.test

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -5,14 +5,14 @@ nextflow_process {
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tag "modules"
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tag "modules_nfcore"
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tag "custom"
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tag "custom/cluster_metrics"
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tag "cluster_metrics"
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tag "custom/clustermetrics"
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tag "clustermetrics"
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test("cluster_metrics - features and clusters") {
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test("clustermetrics - features and clusters") {
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when {
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process {
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"""
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input[0] = [ [id:'test'], file("${projectDir}/modules/nf-core/custom/cluster_metrics/tests/data/test_features.tsv", checkIfExists: true), file("${projectDir}/modules/nf-core/custom/cluster_metrics/tests/data/test_clusters.csv", checkIfExists: true) ]
15+
input[0] = [ [id:'test'], file("${projectDir}/modules/nf-core/custom/clustermetrics/tests/data/test_features.tsv", checkIfExists: true), file("${projectDir}/modules/nf-core/custom/clustermetrics/tests/data/test_clusters.csv", checkIfExists: true) ]
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input[1] = 'test'
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"""
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}
@@ -28,12 +28,12 @@ nextflow_process {
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}
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}
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test("cluster_metrics - features and clusters - stub") {
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test("clustermetrics - features and clusters - stub") {
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options "-stub"
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when {
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process {
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"""
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input[0] = [ [id:'test'], file("${projectDir}/modules/nf-core/custom/cluster_metrics/tests/data/test_features.tsv", checkIfExists: true), file("${projectDir}/modules/nf-core/custom/cluster_metrics/tests/data/test_clusters.csv", checkIfExists: true) ]
36+
input[0] = [ [id:'test'], file("${projectDir}/modules/nf-core/custom/clustermetrics/tests/data/test_features.tsv", checkIfExists: true), file("${projectDir}/modules/nf-core/custom/clustermetrics/tests/data/test_clusters.csv", checkIfExists: true) ]
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input[1] = 'test'
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"""
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}

modules/nf-core/custom/cluster_metrics/tests/main.nf.test.snap renamed to modules/nf-core/custom/clustermetrics/tests/main.nf.test.snap

Lines changed: 48 additions & 48 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,41 @@
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{
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"cluster_metrics - features and clusters - stub": {
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"clustermetrics - features and clusters": {
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"content": [
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[
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[
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{
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"id": "test"
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},
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"test_metrics.tsv:md5,7bfdac9bca90ba2ea3c03eca25b24f28"
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]
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],
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[
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[
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{
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"id": "test"
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},
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"test_k_sweep.csv:md5,8c382a00d959ae5d6e19f42cf9278f37"
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]
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],
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[
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[
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{
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"id": "test"
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},
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"test_selected.json:md5,633493b1585fb0ec0a81629bde4c00cb"
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]
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],
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[
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"versions.yml:md5,00e23b98be698c459e9c94079b0164e0"
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]
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],
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"timestamp": "2026-05-06T17:29:16.510271878",
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"meta": {
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"nf-test": "0.9.5",
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"nextflow": "25.09.0"
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}
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},
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"clustermetrics - features and clusters - stub": {
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"content": [
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{
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"0": [
@@ -32,15 +68,15 @@
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"id": "test"
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},
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[
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"test_calinski.png:md5,9ad4ecb0779b571ed6f869b5523d821c",
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"test_davies_bouldin.png:md5,87eeef85f2bdc97cd3faab3c984fa4cc",
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"test_elbow.png:md5,e1980b81ed477b8defe062f5e1dd9af3",
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"test_silhouette.png:md5,4fff8e7a883ed692329e4d73485e0e50"
71+
"test_calinski.png:md5,a5db5a4340f5a203f8cfb1e27617eab1",
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"test_davies_bouldin.png:md5,b083077c690cc454c7094d6d0c72fdb9",
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"test_elbow.png:md5,e90e14974deb0776c9b784c1de8b8ef0",
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"test_silhouette.png:md5,b7f103711912855f97d8588e1be2d659"
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]
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]
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],
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"4": [
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"versions.yml:md5,7f675f156526d327dab66b3edbcaf81d"
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"versions.yml:md5,00e23b98be698c459e9c94079b0164e0"
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],
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"k_sweep": [
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[
@@ -64,10 +100,10 @@
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"id": "test"
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},
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[
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"test_calinski.png:md5,9ad4ecb0779b571ed6f869b5523d821c",
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"test_davies_bouldin.png:md5,87eeef85f2bdc97cd3faab3c984fa4cc",
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"test_elbow.png:md5,e1980b81ed477b8defe062f5e1dd9af3",
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"test_silhouette.png:md5,4fff8e7a883ed692329e4d73485e0e50"
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"test_calinski.png:md5,a5db5a4340f5a203f8cfb1e27617eab1",
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"test_davies_bouldin.png:md5,b083077c690cc454c7094d6d0c72fdb9",
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"test_elbow.png:md5,e90e14974deb0776c9b784c1de8b8ef0",
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"test_silhouette.png:md5,b7f103711912855f97d8588e1be2d659"
71107
]
72108
]
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],
@@ -80,47 +116,11 @@
80116
]
81117
],
82118
"versions": [
83-
"versions.yml:md5,7f675f156526d327dab66b3edbcaf81d"
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"versions.yml:md5,00e23b98be698c459e9c94079b0164e0"
84120
]
85121
}
86122
],
87-
"timestamp": "2026-05-04T16:19:18.154807795",
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"meta": {
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"nf-test": "0.9.5",
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"nextflow": "25.09.0"
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}
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},
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"cluster_metrics - features and clusters": {
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"content": [
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[
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[
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{
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"id": "test"
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},
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"test_metrics.tsv:md5,7bfdac9bca90ba2ea3c03eca25b24f28"
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]
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],
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[
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[
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{
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"id": "test"
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},
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"test_k_sweep.csv:md5,8c382a00d959ae5d6e19f42cf9278f37"
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]
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],
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[
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[
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{
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"id": "test"
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},
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"test_selected.json:md5,633493b1585fb0ec0a81629bde4c00cb"
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]
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],
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[
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"versions.yml:md5,7f675f156526d327dab66b3edbcaf81d"
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]
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],
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"timestamp": "2026-05-04T16:18:56.462902926",
123+
"timestamp": "2026-05-06T17:29:21.180634202",
124124
"meta": {
125125
"nf-test": "0.9.5",
126126
"nextflow": "25.09.0"

modules/nf-core/custom/cluster_viz/environment.yml renamed to modules/nf-core/custom/clustervisualiation/environment.yml

File renamed without changes.

modules/nf-core/custom/cluster_viz/main.nf renamed to modules/nf-core/custom/clustervisualiation/main.nf

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -33,7 +33,7 @@ process CLUSTER_VIZ {
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def prefix = task.ext.prefix ?: out_prefix ?: "${meta.id}"
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3535
"""
36-
python3 ${projectDir}/modules/nf-core/custom/cluster_viz/templates/cluster_viz.py \\
36+
python3 ${moduleDir}/templates/cluster_viz.py \\
3737
--features ${features} \\
3838
--clusters ${clusters} \\
3939
--pca-scores ${pca_scores} \\

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