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Fix pyclonevi versions on conda and update version (#11761)
* Fix pyclonevi versions on conda and update version * Fix issues with the meta.yml * Indentation
1 parent 54d9a86 commit 9a111d6

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Lines changed: 61 additions & 58 deletions

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‎modules/nf-core/pyclonevi/environment.yml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,5 +3,5 @@ channels:
33
- bioconda
44

55
dependencies:
6-
- bioconda::pyclone-vi=0.1.6
6+
- bioconda::pyclone-vi=0.2.0
77
- conda-forge::numpy=2.0.0

‎modules/nf-core/pyclonevi/main.nf‎

Lines changed: 8 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -3,18 +3,18 @@ process PYCLONEVI {
33
label "process_high"
44
conda "${moduleDir}/environment.yml"
55
container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
6-
'https://depot.galaxyproject.org/singularity/pyclone-vi:0.1.6--pyhdfd78af_0' :
7-
'quay.io/biocontainers/pyclone-vi:0.1.6--pyhdfd78af_0' }"
6+
'https://depot.galaxyproject.org/singularity/pyclone-vi:0.2.0--pyhdfd78af_0' :
7+
'quay.io/biocontainers/pyclone-vi:0.2.0--pyhdfd78af_0' }"
88

99
input:
1010
tuple val(meta), path(rds_join), val(tumour_samples)
1111

1212
output:
13-
tuple val(meta), path("*_cluster_table.csv"), emit: ctree_input
14-
tuple val(meta), path("*.tsv"), emit: pyclone_input
15-
tuple val(meta), path("*_all_fits.h5"), emit: pyclone_all_fits
16-
tuple val(meta), path("*_best_fit.txt"), emit: pyclone_best_fit
17-
path "versions.yml", emit: versions_pyclonevi, topic: versions
13+
tuple val(meta), path("*_cluster_table.csv"), emit: ctree_input
14+
tuple val(meta), path("*.tsv"), emit: pyclone_input
15+
tuple val(meta), path("*_all_fits.h5"), emit: pyclone_all_fits
16+
tuple val(meta), path("*_best_fit.txt"), emit: pyclone_best_fit
17+
path "versions.yml", emit: versions_pyclonevi, topic: versions
1818

1919
when:
2020
task.ext.when == null || task.ext.when
@@ -31,10 +31,9 @@ process PYCLONEVI {
3131
touch ${prefix}_all_fits.h5
3232
touch ${prefix}_best_fit.txt
3333
34-
3534
cat <<-END_VERSIONS > versions.yml
3635
"${task.process}":
37-
pyclonevi: \$( pip show pyclone-vi | grep Version | sed -e "s/Version: //g" )
36+
pyclonevi: \$( pyclone-vi --version | sed "s/.*version //g" )
3837
END_VERSIONS
3938
"""
4039
}

‎modules/nf-core/pyclonevi/meta.yml‎

Lines changed: 4 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -39,8 +39,7 @@ output:
3939
- - meta:
4040
type: map
4141
description: |
42-
Groovy Map containing sample inforSanRafCocoGnd-2024.5
43-
mation
42+
Groovy Map containing sample information
4443
- "*_cluster_table.csv":
4544
type: file
4645
description: Files containing information about identified clusters
@@ -51,8 +50,7 @@ output:
5150
- - meta:
5251
type: map
5352
description: |
54-
Groovy Map containing sample inforSanRafCocoGnd-2024.5
55-
mation
53+
Groovy Map containing sample information
5654
- "*.tsv":
5755
type: file
5856
description: Files containing the input table for pyclone-vi
@@ -62,8 +60,7 @@ output:
6260
- - meta:
6361
type: map
6462
description: |
65-
Groovy Map containing sample inforSanRafCocoGnd-2024.5
66-
mation
63+
Groovy Map containing sample information
6764
- "*_all_fits.h5":
6865
type: file
6966
description: H5 file containing all the pyclone-vi output fits
@@ -73,8 +70,7 @@ output:
7370
- - meta:
7471
type: map
7572
description: |
76-
Groovy Map containing sample inforSanRafCocoGnd-2024.5
77-
mation
73+
Groovy Map containing sample information
7874
- "*_best_fit.txt":
7975
type: file
8076
description: TXT file containing the pyclone-vi best fit.

‎modules/nf-core/pyclonevi/tests/main.nf.test‎

Lines changed: 12 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -10,14 +10,13 @@ nextflow_process {
1010

1111
test("pyclonevi") {
1212

13-
1413
config "./nextflow.config"
1514

1615
when {
1716
process {
1817
"""
1918
input[0] = [
20-
meta = [ id : "test", patient : "HCC1395", tumour_sample : "HCC1395_HCC1395T" ],
19+
[ id : "test", patient : "HCC1395", tumour_sample : "HCC1395_HCC1395T" ],
2120
file(params.modules_testdata_base_path + 'delete_me/pyclonevi/HCC1395_WXS_HCC1395_joint_table.tsv', checkIfExists: true),
2221
[ 'HCC1395_HCC1395T' ]
2322
]
@@ -26,14 +25,13 @@ nextflow_process {
2625
}
2726

2827
then {
28+
assert process.success
2929
assertAll(
30-
{ assert process.success },
31-
{ assert snapshot(process.out.versions_pyclonevi).match() },
32-
{ assert file(process.out.ctree_input[0][1]).exists() },
33-
{ assert file(process.out.pyclone_input[0][1][0]).exists() },
34-
{ assert file(process.out.pyclone_input[0][1][1]).exists() },
35-
{ assert file(process.out.pyclone_all_fits[0][1]).exists() },
36-
{ assert file(process.out.pyclone_best_fit[0][1]).exists() }
30+
{ assert snapshot(
31+
sanitizeOutput(
32+
process.out,
33+
unstableKeys: ["ctree_input", "pyclone_input", "pyclone_all_fits", "pyclone_best_fit"]
34+
)).match() }
3735
)
3836
}
3937

@@ -47,7 +45,7 @@ nextflow_process {
4745
process {
4846
"""
4947
input[0] = [
50-
meta = [ id : "test", patient : "HCC1395", tumour_sample : "HCC1395_HCC1395T" ],
48+
[ id : "test", patient : "HCC1395", tumour_sample : "HCC1395_HCC1395T" ],
5149
file(params.modules_testdata_base_path + 'delete_me/pyclonevi/HCC1395_WXS_HCC1395_joint_table.tsv', checkIfExists: true),
5250
[ 'HCC1395_HCC1395T']
5351
]
@@ -58,7 +56,10 @@ nextflow_process {
5856
then {
5957
assertAll(
6058
{ assert process.success },
61-
{ assert snapshot(process.out).match() }
59+
{ assert snapshot(
60+
sanitizeOutput(process.out),
61+
path(process.out.versions_pyclonevi[0]).yaml
62+
).match() }
6263
)
6364
}
6465

‎modules/nf-core/pyclonevi/tests/main.nf.test.snap‎

Lines changed: 36 additions & 29 deletions
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
22
"pyclonevi - stub": {
33
"content": [
44
{
5-
"0": [
5+
"ctree_input": [
66
[
77
{
88
"id": "test",
@@ -12,47 +12,63 @@
1212
"test_cluster_table.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
1313
]
1414
],
15-
"1": [
15+
"pyclone_all_fits": [
1616
[
1717
{
1818
"id": "test",
1919
"patient": "HCC1395",
2020
"tumour_sample": "HCC1395_HCC1395T"
2121
},
22-
"test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
22+
"test_all_fits.h5:md5,d41d8cd98f00b204e9800998ecf8427e"
2323
]
2424
],
25-
"2": [
25+
"pyclone_best_fit": [
2626
[
2727
{
2828
"id": "test",
2929
"patient": "HCC1395",
3030
"tumour_sample": "HCC1395_HCC1395T"
3131
},
32-
"test_all_fits.h5:md5,d41d8cd98f00b204e9800998ecf8427e"
32+
"test_best_fit.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
3333
]
3434
],
35-
"3": [
35+
"pyclone_input": [
3636
[
3737
{
3838
"id": "test",
3939
"patient": "HCC1395",
4040
"tumour_sample": "HCC1395_HCC1395T"
4141
},
42-
"test_best_fit.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
42+
"test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
4343
]
4444
],
45-
"4": [
45+
"versions_pyclonevi": [
4646
"versions.yml:md5,d7a72f90b5e871ad593d6b02ac78abb4"
47-
],
47+
]
48+
},
49+
{
50+
"PYCLONEVI": {
51+
"pyclonevi": "0.1.6"
52+
}
53+
}
54+
],
55+
"timestamp": "2026-05-26T11:01:04.192976421",
56+
"meta": {
57+
"nf-test": "0.9.5",
58+
"nextflow": "26.04.0"
59+
}
60+
},
61+
"pyclonevi": {
62+
"content": [
63+
{
4864
"ctree_input": [
4965
[
5066
{
5167
"id": "test",
5268
"patient": "HCC1395",
5369
"tumour_sample": "HCC1395_HCC1395T"
5470
},
55-
"test_cluster_table.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
71+
"test_cluster_table.csv"
5672
]
5773
],
5874
"pyclone_all_fits": [
@@ -62,7 +78,7 @@
6278
"patient": "HCC1395",
6379
"tumour_sample": "HCC1395_HCC1395T"
6480
},
65-
"test_all_fits.h5:md5,d41d8cd98f00b204e9800998ecf8427e"
81+
"test_all_fits.h5"
6682
]
6783
],
6884
"pyclone_best_fit": [
@@ -72,7 +88,7 @@
7288
"patient": "HCC1395",
7389
"tumour_sample": "HCC1395_HCC1395T"
7490
},
75-
"test_best_fit.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
91+
"test_best_fit.txt"
7692
]
7793
],
7894
"pyclone_input": [
@@ -82,30 +98,21 @@
8298
"patient": "HCC1395",
8399
"tumour_sample": "HCC1395_HCC1395T"
84100
},
85-
"test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
101+
[
102+
"test_pyclone_input.tsv",
103+
"test_pyclone_input_all_samples.tsv"
104+
]
86105
]
87106
],
88107
"versions_pyclonevi": [
89-
"versions.yml:md5,d7a72f90b5e871ad593d6b02ac78abb4"
108+
"versions.yml:md5,764c065f67a1502d5158a8a018d8a388"
90109
]
91110
}
92111
],
93-
"timestamp": "2026-03-06T18:18:08.188467",
94-
"meta": {
95-
"nf-test": "0.9.4",
96-
"nextflow": "25.10.0"
97-
}
98-
},
99-
"pyclonevi": {
100-
"content": [
101-
[
102-
"versions.yml:md5,764c065f67a1502d5158a8a018d8a388"
103-
]
104-
],
105-
"timestamp": "2026-03-06T18:40:05.865588",
112+
"timestamp": "2026-05-26T11:00:56.527463061",
106113
"meta": {
107-
"nf-test": "0.9.4",
108-
"nextflow": "25.10.0"
114+
"nf-test": "0.9.5",
115+
"nextflow": "26.04.0"
109116
}
110117
}
111118
}

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