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

Nf test local modules #223

Open
wants to merge 5 commits into
base: new-output-dir
Choose a base branch
from
+1,039 −2
Open

Nf test local modules #223

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
597a12e
automap tests
nvnieuwk Nov 13, 2024
b896143
test filter_beds
nvnieuwk Nov 13, 2024
4f200f1
test updio and merge_beds
nvnieuwk Nov 14, 2024
f6165bf
pre-commit
nvnieuwk Nov 14, 2024
da5d1f8
update rtgtools/format
nvnieuwk Nov 14, 2024
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
2 changes: 1 addition & 1 deletion modules.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -137,7 +137,7 @@
},
"rtgtools/format": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "167a20a2e267261af397e9ea5bf58426e6345ce7",
"installed_by": ["modules"]
},
"rtgtools/pedfilter": {
Expand Down
95 changes: 95 additions & 0 deletions modules/local/automap/automap/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,95 @@
nextflow_process {

name "Test Process AUTOMAP_AUTOMAP"
script "../main.nf"
process "AUTOMAP_AUTOMAP"

tag "modules"
tag "modules_local"
tag "automap"
tag "automap/automap"

setup {
run("AUTOMAP_REPEATS") {
script "../../repeats/main.nf"
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
"hg38"
]
"""
}
}
}

test("homo_sapiens - vcf, tbi, repeats, [], hg38") {

config "./nextflow.config"

when {
process {
"""
input[0] = [
[ id:'test', family_samples:"NA24143,NA24149,NA24385", caller:"haplotypecaller" ], // meta map
file(params.famvcf, checkIfExists: true),
file(params.famtbi, checkIfExists: true)
]
input[1] = AUTOMAP_REPEATS.out.repeats
input[2] = [[],[]]
input[3] = "hg38"
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.automap.collect { meta, out ->
[
meta,
path(out).list().collect {
it.list().collect {
"${file(it.toString()).name},variantsMD5:${it.vcf.variantsMD5}"
}
}
]
},
process.out.versions
).match() }
)
}

}

test("homo_sapiens - vcf, tbi, repeats, [], hg38 - stub") {

options "-stub"
config "./nextflow.config"

when {
process {
"""
input[0] = [
[ id:'test', family_samples:"NA24143,NA24149,NA24385", caller:"haplotypecaller" ], // meta map
file(params.famvcf, checkIfExists: true),
file(params.famtbi, checkIfExists: true)
]
input[1] = AUTOMAP_REPEATS.out.repeats
input[2] = [[],[]]
input[3] = "hg38"
"""
}
}

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

}

}
109 changes: 109 additions & 0 deletions modules/local/automap/automap/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,109 @@
{
"homo_sapiens - vcf, tbi, repeats, [], hg38": {
"content": [
[
[
{
"id": "test",
"family_samples": "NA24143,NA24149,NA24385",
"caller": "haplotypecaller"
},
[
[
"NA24143.individual.vcf,variantsMD5:d87c6d5aea196c746312a8a383eede4b"
],
[
"NA24149.individual.vcf,variantsMD5:24eacd6958a767b7768b4282caea52cc"
],
[
"NA24385.individual.vcf,variantsMD5:f7f27a20139824e3e49cf17a2867489b"
]
]
]
],
[
"versions.yml:md5,8d88bdf05fc6f578d81fee3716f8b562"
]
],
"meta": {
"nf-test": "0.9.1",
"nextflow": "24.10.0"
},
"timestamp": "2024-11-13T17:03:29.44273724"
},
"homo_sapiens - vcf, tbi, repeats, [], hg38 - stub": {
"content": [
{
"0": [
[
{
"id": "test",
"family_samples": "NA24143,NA24149,NA24385",
"caller": "haplotypecaller"
},
[
[
"sample1.HomRegions.cmgg_bio.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
"sample1.HomRegions.pdf:md5,d41d8cd98f00b204e9800998ecf8427e",
"sample1.HomRegions.strict.cmgg_bio.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
"sample1.HomRegions.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
],
[
"sample2.HomRegions.cmgg_bio.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
"sample2.HomRegions.pdf:md5,d41d8cd98f00b204e9800998ecf8427e",
"sample2.HomRegions.strict.cmgg_bio.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
"sample2.HomRegions.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
],
[
"sample3.HomRegions.cmgg_bio.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
"sample3.HomRegions.pdf:md5,d41d8cd98f00b204e9800998ecf8427e",
"sample3.HomRegions.strict.cmgg_bio.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
"sample3.HomRegions.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
]
],
"1": [
"versions.yml:md5,8d88bdf05fc6f578d81fee3716f8b562"
],
"automap": [
[
{
"id": "test",
"family_samples": "NA24143,NA24149,NA24385",
"caller": "haplotypecaller"
},
[
[
"sample1.HomRegions.cmgg_bio.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
"sample1.HomRegions.pdf:md5,d41d8cd98f00b204e9800998ecf8427e",
"sample1.HomRegions.strict.cmgg_bio.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
"sample1.HomRegions.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
],
[
"sample2.HomRegions.cmgg_bio.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
"sample2.HomRegions.pdf:md5,d41d8cd98f00b204e9800998ecf8427e",
"sample2.HomRegions.strict.cmgg_bio.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
"sample2.HomRegions.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
],
[
"sample3.HomRegions.cmgg_bio.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
"sample3.HomRegions.pdf:md5,d41d8cd98f00b204e9800998ecf8427e",
"sample3.HomRegions.strict.cmgg_bio.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
"sample3.HomRegions.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
]
],
"versions": [
"versions.yml:md5,8d88bdf05fc6f578d81fee3716f8b562"
]
}
],
"meta": {
"nf-test": "0.9.1",
"nextflow": "24.10.0"
},
"timestamp": "2024-11-13T17:00:28.503010269"
}
}
5 changes: 5 additions & 0 deletions modules/local/automap/automap/tests/nextflow.config
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
process {
withName: "AUTOMAP_AUTOMAP" {
ext.args = "--panelname cmgg_bio --multivcf"
}
}
58 changes: 58 additions & 0 deletions modules/local/automap/repeats/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,58 @@
nextflow_process {

name "Test Process AUTOMAP_REPEATS"
script "../main.nf"
process "AUTOMAP_REPEATS"

tag "modules"
tag "modules_local"
tag "automap"
tag "automap/repeats"

test("homo_sapiens - hg38") {

when {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
"hg38"
]
"""
}
}

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

}

test("homo_sapiens - hg38 - stub") {

options "-stub"

when {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
"hg38"
]
"""
}
}

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

}

}
72 changes: 72 additions & 0 deletions modules/local/automap/repeats/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,72 @@
{
"homo_sapiens - hg38": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
"test.bed:md5,74190e74851226329342a3fcae133cdb"
]
],
"1": [
"versions.yml:md5,b5fc7b6bfce18165907357d8966f09d4"
],
"repeats": [
[
{
"id": "test",
"single_end": false
},
"test.bed:md5,74190e74851226329342a3fcae133cdb"
]
],
"versions": [
"versions.yml:md5,b5fc7b6bfce18165907357d8966f09d4"
]
}
],
"meta": {
"nf-test": "0.9.1",
"nextflow": "24.10.0"
},
"timestamp": "2024-11-13T16:31:33.522485317"
},
"homo_sapiens - hg38 - stub": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
"test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"versions.yml:md5,b5fc7b6bfce18165907357d8966f09d4"
],
"repeats": [
[
{
"id": "test",
"single_end": false
},
"test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,b5fc7b6bfce18165907357d8966f09d4"
]
}
],
"meta": {
"nf-test": "0.9.1",
"nextflow": "24.10.0"
},
"timestamp": "2024-11-13T16:31:43.895708133"
}
}
Loading
Loading