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Swap tinc to topics and pin conda versions (#11762)
* Swap tinc to topics and pin conda versions * Update modules/nf-core/tinc/environment.yml * Fix linting --------- Co-authored-by: Lucrezia Valeriani <valerianilucrezia11@gmail.com>
1 parent 8d62f18 commit 0d51a46

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Lines changed: 63 additions & 77 deletions

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‎modules/nf-core/tinc/environment.yml‎

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,9 @@
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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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channels:
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- conda-forge
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- bioconda
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dependencies:
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- "bioconda::r-tinc=0.1.0"
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- bioconda::r-cnaqc=1.1.2
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- bioconda::r-tinc=0.1.0
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- conda-forge::r-tidyverse=2.0.0

‎modules/nf-core/tinc/main.nf‎

Lines changed: 8 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -13,11 +13,11 @@ process TINC {
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tuple val(meta), path(cna_rds), path(vcf_rds)
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output:
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tuple val(meta), path("*_fit.rds"), emit: rds
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tuple val(meta), path("*_plot.rds"), emit: plot_rds
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tuple val(meta), path("*.pdf"), emit: plot_pdf
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tuple val(meta), path("*_qc.csv"), emit: tinc_csv
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path "versions.yml", emit: versions
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tuple val(meta), path("*_fit.rds"), emit: rds
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tuple val(meta), path("*_plot.rds"), emit: plot_rds
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tuple val(meta), path("*.pdf"), emit: plot_pdf
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tuple val(meta), path("*_qc.csv"), emit: tinc_csv
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path "versions.yml", emit: versions_tinc, topic: versions
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when:
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task.ext.when == null || task.ext.when
@@ -36,7 +36,9 @@ process TINC {
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bioconductor-rtinc: \$(Rscript -e "library(TINC); cat(as.character(packageVersion('TINC')))")
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TINC: \$(Rscript -e "library(TINC); cat(as.character(packageVersion('TINC')))")
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tidyverse: \$(Rscript -e "cat(as.character(packageVersion('tidyverse')))")
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CNAqc: \$(Rscript -e "cat(as.character(packageVersion('CNAqc')))")
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END_VERSIONS
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"""
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}

‎modules/nf-core/tinc/meta.yml‎

Lines changed: 15 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,12 @@
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name: "tinc"
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description: "TINC is a package to determine the contamination of tumour DNA in a matched normal sample. The approach uses evolutionary theory applied to read counts data from whole-genome sequencing assays."
2+
description: "TINC is a package to determine the contamination of tumour DNA in a
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matched normal sample. The approach uses evolutionary theory applied to read counts
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data from whole-genome sequencing assays."
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keywords:
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- genomics
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- tumour contamination
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- normal
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- purity
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tools:
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- "tinc":
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description: "TINC is a package that implements algorithms to determine the contamination
@@ -21,25 +22,22 @@ tools:
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documentation: "https://caravagnalab.github.io/TINC/"
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tool_dev_url: "https://github.com/caravagnalab/TINC/"
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doi: "10.1038/s41467-023-44158-2"
24-
licence: ["GPL v3"]
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licence:
26+
- "GPL v3"
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identifier: "biotools:r-tinc"
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input:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1', tumour_sample:'tumour_sample1_name', normal_sample:'normal_sample_name' ]`
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- cna_rds:
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type: file
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description: RDS file with copy number segments and purity
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ontologies: []
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- vcf_rds:
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type: file
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description: RDS file with vcf calls from tumour and normal sample
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ontologies: []
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output:
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rds:
@@ -63,7 +61,6 @@ output:
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type: file
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description: RDS file with the plot of the results
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pattern: "*.{rds}"
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ontologies: []
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plot_pdf:
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- - meta:
@@ -86,17 +83,23 @@ output:
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type: file
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description: CSV file with the output of TINC qc flag
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pattern: "*.{csv}"
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ontologies:
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- edam: http://edamontology.org/format_3752 # CSV
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- edam: http://edamontology.org/format_3752
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versions_tinc:
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- versions.yml:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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ontologies:
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- edam: http://edamontology.org/format_3750
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topics:
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versions:
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- versions.yml:
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type: file
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description: File containing software versions
96100
pattern: "versions.yml"
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ontologies:
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- edam: http://edamontology.org/format_3750 # YAML
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- edam: http://edamontology.org/format_3750
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authors:
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- "@valerianilucrezia"
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maintainers:

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

Lines changed: 6 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -33,7 +33,8 @@ nextflow_process {
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assertAll(
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{ assert process.success },
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{ assert snapshot(
36-
process.out.versions
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process.out.findAll { key, val -> key.startsWith('versions') },
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path(process.out.versions_tinc[0]).yaml
3738
).match() },
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{ assert file(process.out.rds[0][1]).exists() },
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{ assert file(process.out.plot_rds[0][1]).exists() },
@@ -62,7 +63,10 @@ nextflow_process {
6263
then {
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assertAll(
6465
{ assert process.success },
65-
{ assert snapshot(process.out).match() }
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{ assert snapshot(
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sanitizeOutput(process.out),
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path(process.out.versions_tinc[0]).yaml
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).match() }
6670
)
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}
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‎modules/nf-core/tinc/tests/main.nf.test.snap‎

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Original file line numberDiff line numberDiff line change
@@ -1,62 +1,28 @@
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{
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"tinc - rds": {
33
"content": [
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[
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"versions.yml:md5,fd8574ef3613bda9da0db50875ab36fc"
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]
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{
5+
"versions_tinc": [
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"versions.yml:md5,fd8574ef3613bda9da0db50875ab36fc"
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]
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},
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{
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"TINC": {
11+
"CNAqc": "1.1.2",
12+
"tidyverse": "2.0.0",
13+
"TINC": "0.1.0"
14+
}
15+
}
716
],
17+
"timestamp": "2026-05-26T11:17:23.848447266",
818
"meta": {
9-
"nf-test": "0.9.2",
10-
"nextflow": "24.10.3"
11-
},
12-
"timestamp": "2025-06-23T17:19:07.295163"
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"nf-test": "0.9.5",
20+
"nextflow": "26.04.0"
21+
}
1322
},
1423
"tinc - rds - stub": {
1524
"content": [
1625
{
17-
"0": [
18-
[
19-
{
20-
"id": "test",
21-
"tumour_sample": "HCC1395_HCC1395T",
22-
"normal_sample": "HCC1395_HCC1395N"
23-
},
24-
"test_fit.rds:md5,d41d8cd98f00b204e9800998ecf8427e"
25-
]
26-
],
27-
"1": [
28-
[
29-
{
30-
"id": "test",
31-
"tumour_sample": "HCC1395_HCC1395T",
32-
"normal_sample": "HCC1395_HCC1395N"
33-
},
34-
"test_plot.rds:md5,d41d8cd98f00b204e9800998ecf8427e"
35-
]
36-
],
37-
"2": [
38-
[
39-
{
40-
"id": "test",
41-
"tumour_sample": "HCC1395_HCC1395T",
42-
"normal_sample": "HCC1395_HCC1395N"
43-
},
44-
"test.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
45-
]
46-
],
47-
"3": [
48-
[
49-
{
50-
"id": "test",
51-
"tumour_sample": "HCC1395_HCC1395T",
52-
"normal_sample": "HCC1395_HCC1395N"
53-
},
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"test_qc.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
55-
]
56-
],
57-
"4": [
58-
"versions.yml:md5,794f464ec69ce573be2d9052659964f2"
59-
],
6026
"plot_pdf": [
6127
[
6228
{
@@ -97,15 +63,22 @@
9763
"test_qc.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
9864
]
9965
],
100-
"versions": [
101-
"versions.yml:md5,794f464ec69ce573be2d9052659964f2"
66+
"versions_tinc": [
67+
"versions.yml:md5,092df7ac0ff11e3d2be5cb38671e5e80"
10268
]
69+
},
70+
{
71+
"TINC": {
72+
"TINC": "0.1.0",
73+
"tidyverse": "2.0.0",
74+
"CNAqc": "1.1.2"
75+
}
10376
}
10477
],
78+
"timestamp": "2026-05-26T11:17:34.699461564",
10579
"meta": {
106-
"nf-test": "0.9.2",
107-
"nextflow": "24.10.3"
108-
},
109-
"timestamp": "2025-06-16T18:34:44.017922"
80+
"nf-test": "0.9.5",
81+
"nextflow": "26.04.0"
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}
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}
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}

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