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Merge branch 'master' into oncocnv-#7657 
2 parents 3150810 + f63c350 commit aaf5253

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11 files changed

+236
-57
lines changed

11 files changed

+236
-57
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‎.github/skip_nf_test.json

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Original file line numberDiff line numberDiff line change
@@ -21,6 +21,7 @@
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"modules/nf-core/cellrangerarc/mkref",
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"modules/nf-core/cellrangerarc/count",
2323
"modules/nf-core/cellrangerarc/mkgtf",
24+
"modules/nf-core/cellrangeratac/mkfastq",
2425
"modules/nf-core/cellrangeratac/mkref",
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"modules/nf-core/checkqc",
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"modules/nf-core/coreograph",

‎modules/nf-core/catpack/download/main.nf

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Original file line numberDiff line numberDiff line change
@@ -24,7 +24,7 @@ process CATPACK_DOWNLOAD {
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CAT_pack \\
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download \\
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${args} \\
27-
--db ${db}
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--db ${db} \\
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-o ${prefix}/
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cat <<-END_VERSIONS > versions.yml

‎modules/nf-core/cellrangeratac/mkfastq/main.nf

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -2,8 +2,7 @@ process CELLRANGERATAC_MKFASTQ {
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tag "mkfastq"
33
label 'process_medium'
44

5-
container "nf-core/cellranger-atac:2.1.0"
6-
5+
container "nf-core/cellranger-atac-mkfastq:2.1.0"
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// Exit if running this module with -profile conda / -profile mamba
87
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
98
error "CELLRANGERATAC_MKFASTQ module does not support Conda. Please use Docker / Singularity / Podman instead."

‎modules/nf-core/cellrangeratac/mkfastq/meta.yml

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Original file line numberDiff line numberDiff line change
@@ -22,25 +22,28 @@ input:
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type: file
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description: Base call files
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pattern: "*.bcl.bgzf"
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ontologies: []
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- - csv:
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type: file
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description: Sample sheet
2829
pattern: "*.csv"
30+
ontologies:
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- edam: http://edamontology.org/format_3752 # CSV
2932
output:
3033
- versions:
3134
- versions.yml:
3235
type: file
3336
description: File containing software version
3437
pattern: "versions.yml"
38+
ontologies:
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- edam: http://edamontology.org/format_3750 # YAML
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- fastq:
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- ${bcl.getSimpleName(:
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type: file
3843
description: Unaligned FastQ files
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pattern: "*.fastq.gz"
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- /*.fastq.gz:
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type: file
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description: Unaligned FastQ files
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pattern: "*.fastq.gz"
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ontologies:
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- edam: http://edamontology.org/format_3989 # GZIP format
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authors:
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- "@ggabernet"
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- "@edmundmiller"

‎modules/nf-core/cellrangeratac/mkfastq/tests/main.nf.test

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,110 @@
1+
nextflow_process {
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3+
name "Test Process CELLRANGERATAC_MKFASTQ"
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5+
script "../main.nf"
6+
process "CELLRANGERATAC_MKFASTQ"
7+
8+
tag "modules"
9+
tag "modules_nfcore"
10+
tag "untar"
11+
tag "cellrangeratac"
12+
tag "cellrangeratac/mkfastq"
13+
14+
setup {
15+
run("UNTAR") {
16+
script "../../../untar/main.nf"
17+
18+
process {
19+
"""
20+
input[0] = [[],file("https://cf.10xgenomics.com/supp/cell-atac/cellranger-atac-tiny-bcl-1.0.0.tar.gz", checkIfExists:true)]
21+
"""
22+
}
23+
}
24+
}
25+
26+
test("test_cellrangeratac_mkfastq_simple") {
27+
28+
when {
29+
process {
30+
"""
31+
input[0] = UNTAR.out.untar.map{it[1]}
32+
input[1] = file("https://cf.10xgenomics.com/supp/cell-atac/cellranger-atac-tiny-bcl-simple-1.0.0.csv", checkIfExists:true)
33+
"""
34+
}
35+
}
36+
then {
37+
assertAll(
38+
{ assert process.success },
39+
{ assert snapshot(process.out).match() }
40+
)
41+
}
42+
}
43+
setup {
44+
run("UNTAR") {
45+
script "../../../untar/main.nf"
46+
47+
process {
48+
"""
49+
input[0] = [[],file("https://cf.10xgenomics.com/supp/cell-atac/cellranger-atac-tiny-bcl-1.0.0.tar.gz", checkIfExists:true)]
50+
"""
51+
}
52+
}
53+
}
54+
55+
test("test_cellrangeratac_mkfastq_illumina") {
56+
57+
when {
58+
process {
59+
"""
60+
input[0] = UNTAR.out.untar.map{it[1]}
61+
input[1] = file("https://cf.10xgenomics.com/supp/cell-atac/cellranger-atac-tiny-bcl-samplesheet-1.0.0.csv", checkIfExists:true)
62+
"""
63+
}
64+
}
65+
then {
66+
assertAll(
67+
{ assert process.success },
68+
{ assert snapshot(process.out).match() }
69+
)
70+
}
71+
}
72+
73+
74+
test("test_cellrangeratac_mkfastq_simple -- stub") {
75+
options '-stub'
76+
when {
77+
process {
78+
"""
79+
input[0] = UNTAR.out.untar.map{it[1]}
80+
input[1] = file("https://cf.10xgenomics.com/supp/cell-atac/cellranger-atac-tiny-bcl-simple-1.0.0.csv", checkIfExists:true)
81+
"""
82+
}
83+
}
84+
then {
85+
assertAll(
86+
{ assert process.success },
87+
{ assert snapshot(process.out).match() }
88+
)
89+
}
90+
}
91+
92+
93+
test("test_cellrangeratac_mkfastq_illumina -- stub") {
94+
options '-stub'
95+
when {
96+
process {
97+
"""
98+
input[0] = UNTAR.out.untar.map{it[1]}
99+
input[1] = file("https://cf.10xgenomics.com/supp/cell-atac/cellranger-atac-tiny-bcl-samplesheet-1.0.0.csv",checkIfExists:true)
100+
"""
101+
}
102+
}
103+
then {
104+
assertAll(
105+
{ assert process.success },
106+
{ assert snapshot(process.out).match() }
107+
)
108+
}
109+
}
110+
}

‎modules/nf-core/cellrangeratac/mkfastq/tests/main.nf.test.snap

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@@ -0,0 +1,114 @@
1+
{
2+
"test_cellrangeratac_mkfastq_illumina": {
3+
"content": [
4+
{
5+
"0": [
6+
"versions.yml:md5,b1cead7bb4e583a833825c926cb0cabb"
7+
],
8+
"1": [
9+
[
10+
"Undetermined_S0_L001_I1_001.fastq.gz:md5,297b3a22fbb7fff28439f1d394e597ce",
11+
"Undetermined_S0_L001_R1_001.fastq.gz:md5,230ccefeed90a1f2e7f50c253b4e787b",
12+
"Undetermined_S0_L001_R2_001.fastq.gz:md5,6fdc386e1a7d7a64ac80df462a38bc9a",
13+
"Undetermined_S0_L001_R3_001.fastq.gz:md5,785dd14bfac26d4cea4c0a4f32b42b91"
14+
]
15+
],
16+
"fastq": [
17+
[
18+
"Undetermined_S0_L001_I1_001.fastq.gz:md5,297b3a22fbb7fff28439f1d394e597ce",
19+
"Undetermined_S0_L001_R1_001.fastq.gz:md5,230ccefeed90a1f2e7f50c253b4e787b",
20+
"Undetermined_S0_L001_R2_001.fastq.gz:md5,6fdc386e1a7d7a64ac80df462a38bc9a",
21+
"Undetermined_S0_L001_R3_001.fastq.gz:md5,785dd14bfac26d4cea4c0a4f32b42b91"
22+
]
23+
],
24+
"versions": [
25+
"versions.yml:md5,b1cead7bb4e583a833825c926cb0cabb"
26+
]
27+
}
28+
],
29+
"meta": {
30+
"nf-test": "0.9.2",
31+
"nextflow": "25.04.1"
32+
},
33+
"timestamp": "2025-05-14T09:01:23.08290199"
34+
},
35+
"test_cellrangeratac_mkfastq_simple": {
36+
"content": [
37+
{
38+
"0": [
39+
"versions.yml:md5,b1cead7bb4e583a833825c926cb0cabb"
40+
],
41+
"1": [
42+
[
43+
"Undetermined_S0_L001_I1_001.fastq.gz:md5,297b3a22fbb7fff28439f1d394e597ce",
44+
"Undetermined_S0_L001_R1_001.fastq.gz:md5,230ccefeed90a1f2e7f50c253b4e787b",
45+
"Undetermined_S0_L001_R2_001.fastq.gz:md5,6fdc386e1a7d7a64ac80df462a38bc9a",
46+
"Undetermined_S0_L001_R3_001.fastq.gz:md5,785dd14bfac26d4cea4c0a4f32b42b91"
47+
]
48+
],
49+
"fastq": [
50+
[
51+
"Undetermined_S0_L001_I1_001.fastq.gz:md5,297b3a22fbb7fff28439f1d394e597ce",
52+
"Undetermined_S0_L001_R1_001.fastq.gz:md5,230ccefeed90a1f2e7f50c253b4e787b",
53+
"Undetermined_S0_L001_R2_001.fastq.gz:md5,6fdc386e1a7d7a64ac80df462a38bc9a",
54+
"Undetermined_S0_L001_R3_001.fastq.gz:md5,785dd14bfac26d4cea4c0a4f32b42b91"
55+
]
56+
],
57+
"versions": [
58+
"versions.yml:md5,b1cead7bb4e583a833825c926cb0cabb"
59+
]
60+
}
61+
],
62+
"meta": {
63+
"nf-test": "0.9.2",
64+
"nextflow": "25.04.1"
65+
},
66+
"timestamp": "2025-05-14T08:59:44.975810932"
67+
},
68+
"test_cellrangeratac_mkfastq_simple -- stub": {
69+
"content": [
70+
{
71+
"0": [
72+
"versions.yml:md5,b1cead7bb4e583a833825c926cb0cabb"
73+
],
74+
"1": [
75+
"fake_file.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
76+
],
77+
"fastq": [
78+
"fake_file.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
79+
],
80+
"versions": [
81+
"versions.yml:md5,b1cead7bb4e583a833825c926cb0cabb"
82+
]
83+
}
84+
],
85+
"meta": {
86+
"nf-test": "0.9.2",
87+
"nextflow": "25.04.1"
88+
},
89+
"timestamp": "2025-05-14T09:03:44.373589132"
90+
},
91+
"test_cellrangeratac_mkfastq_illumina -- stub": {
92+
"content": [
93+
{
94+
"0": [
95+
"versions.yml:md5,b1cead7bb4e583a833825c926cb0cabb"
96+
],
97+
"1": [
98+
"fake_file.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
99+
],
100+
"fastq": [
101+
"fake_file.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
102+
],
103+
"versions": [
104+
"versions.yml:md5,b1cead7bb4e583a833825c926cb0cabb"
105+
]
106+
}
107+
],
108+
"meta": {
109+
"nf-test": "0.9.2",
110+
"nextflow": "25.04.1"
111+
},
112+
"timestamp": "2025-05-14T09:06:04.42054523"
113+
}
114+
}

‎modules/nf-core/gatk4/baserecalibrator/meta.yml

Lines changed: 2 additions & 2 deletions
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@@ -68,7 +68,7 @@ input:
6868
e.g. [ id:'genome']
6969
- known_sites:
7070
type: file
71-
description: VCF files with known sites for indels / snps (optional)
71+
description: VCF files with known sites for indels / snps
7272
pattern: "*.vcf.gz"
7373
- - meta6:
7474
type: map
@@ -77,7 +77,7 @@ input:
7777
e.g. [ id:'genome']
7878
- known_sites_tbi:
7979
type: file
80-
description: Tabix index of the known_sites (optional)
80+
description: Tabix index of the known_sites
8181
pattern: "*.vcf.gz.tbi"
8282
output:
8383
- table:

‎tests/config/pytest_modules.yml

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Original file line numberDiff line numberDiff line change
@@ -4,9 +4,6 @@ cellrangerarc/mkfastq:
44
cellrangeratac/count:
55
- modules/nf-core/cellrangeratac/count/**
66
- tests/modules/nf-core/cellrangeratac/count/**
7-
cellrangeratac/mkfastq:
8-
- modules/nf-core/cellrangeratac/mkfastq/**
9-
- tests/modules/nf-core/cellrangeratac/mkfastq/**
107
gangstr:
118
- modules/nf-core/gangstr/**
129
- tests/modules/nf-core/gangstr/**

‎tests/modules/nf-core/cellrangeratac/mkfastq/main.nf

Lines changed: 0 additions & 26 deletions
This file was deleted.

‎tests/modules/nf-core/cellrangeratac/mkfastq/nextflow.config

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This file was deleted.

‎tests/modules/nf-core/cellrangeratac/mkfastq/test.yml

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This file was deleted.

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