Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

update peddy tests #5880

Merged
merged 1 commit into from
Jun 25, 2024
Merged

update peddy tests #5880

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 5 additions & 2 deletions modules/nf-core/peddy/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ process PEDDY {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
peddy: \$( peddy --version 2>&1 | sed 's/peddy, version //' )
peddy: \$( peddy --version 2>&1 | tail -1 | sed 's/peddy, version //' )
END_VERSIONS
"""

Expand All @@ -49,6 +49,9 @@ process PEDDY {
touch ${prefix}.peddy.ped
touch ${prefix}.html

touch versions.yml
cat <<-END_VERSIONS > versions.yml
"${task.process}":
peddy: \$( peddy --version 2>&1 | tail -1 | sed 's/peddy, version //' )
END_VERSIONS
"""
}
35 changes: 35 additions & 0 deletions modules/nf-core/peddy/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,35 @@
nextflow_process {

name "Test Process PEDDY"
script "modules/nf-core/peddy/main.nf"
process "PEDDY"

tag "modules"
tag "modules_nfcore"
tag "peddy"

test("test - peddy - stub") {

options "-stub"

when {
process {
"""
input[0] = [
[ id:'test', single_end:false ],
file(params.test_data['homo_sapiens']['genome']['justhusky_minimal_vcf_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['justhusky_minimal_vcf_gz_tbi'], checkIfExists: true)
]
input[1] = file(params.test_data['homo_sapiens']['genome']['justhusky_ped'], checkIfExists: true)
"""
}
}

then {
assert process.success
assert snapshot(process.out).match()
}

}

}
93 changes: 93 additions & 0 deletions modules/nf-core/peddy/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,93 @@
{
"test - peddy - stub": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
[
"test.html:md5,d41d8cd98f00b204e9800998ecf8427e",
"test.vs.html:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
],
"1": [
[
{
"id": "test",
"single_end": false
},
[
"test.het_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
"test.ped_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
"test.sex_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
],
"2": [
[
{
"id": "test",
"single_end": false
},
"test.peddy.ped:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"3": [

],
"4": [
"versions.yml:md5,d3587e67aded68bcf24c47542efe012f"
],
"csv": [
[
{
"id": "test",
"single_end": false
},
[
"test.het_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
"test.ped_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
"test.sex_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
],
"html": [
[
{
"id": "test",
"single_end": false
},
[
"test.html:md5,d41d8cd98f00b204e9800998ecf8427e",
"test.vs.html:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
],
"ped": [
[
{
"id": "test",
"single_end": false
},
"test.peddy.ped:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"png": [

],
"versions": [
"versions.yml:md5,d3587e67aded68bcf24c47542efe012f"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-06-25T09:28:05.418978589"
}
}
2 changes: 2 additions & 0 deletions modules/nf-core/peddy/tests/tags.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
mosdepth:
- "modules/nf-core/peddy/**"
3 changes: 0 additions & 3 deletions tests/config/pytest_modules.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1197,9 +1197,6 @@ pbbam/pbmerge:
pbptyper:
- modules/nf-core/pbptyper/**
- tests/modules/nf-core/pbptyper/**
peddy:
- modules/nf-core/peddy/**
- tests/modules/nf-core/peddy/**
peka:
- modules/nf-core/peka/**
- tests/modules/nf-core/peka/**
Expand Down
17 changes: 0 additions & 17 deletions tests/modules/nf-core/peddy/main.nf
View file
Open in desktop

This file was deleted.

5 changes: 0 additions & 5 deletions tests/modules/nf-core/peddy/nextflow.config
View file
Open in desktop

This file was deleted.

24 changes: 0 additions & 24 deletions tests/modules/nf-core/peddy/test.yml
View file
Open in desktop

This file was deleted.

Loading