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Update purecn/coverage to nf-test #7308

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merged 11 commits into from
Mar 11, 2025
Merged

Update purecn/coverage to nf-test #7308

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083bb66
Update purecn/coverage to nf-test
SPPearce Jan 15, 2025
974606c
Update snapshot
SPPearce Jan 15, 2025
62d2a66
Merge branch 'master' into purecn_coverage
SPPearce Jan 15, 2025
154da42
Add bioconda to environment requirement
SPPearce Jan 16, 2025
ba61c5d
Update tests
SPPearce Mar 7, 2025
b7741da
Merge branch 'master' into purecn_coverage
SPPearce Mar 10, 2025
987302d
Bump versions and swap to seqera containers
SPPearce Mar 11, 2025
d498079
Merge branch 'master' into purecn_coverage
SPPearce Mar 11, 2025
3979cd4
Update modules/nf-core/purecn/coverage/environment.yml
SPPearce Mar 11, 2025
7ecf0e2
Fix environment
SPPearce Mar 11, 2025
02fd86d
Merge branch 'master' into purecn_coverage
SPPearce Mar 11, 2025
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10 changes: 6 additions & 4 deletions modules/nf-core/purecn/coverage/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,9 @@ channels:
- bioconda

dependencies:
- bioconda::bioconductor-org.hs.eg.db=3.16.0
- bioconda::bioconductor-purecn=2.4.0
- bioconda::bioconductor-txdb.hsapiens.ucsc.hg38.knowngene=3.16.0
- bioconductor-txdb.hsapiens.ucsc.hg19.knowngene=3.2.2
- bioconda::bioconductor-org.hs.eg.db=3.20.0
- bioconda::bioconductor-purecn=2.12.0
- bioconda::bioconductor-txdb.hsapiens.ucsc.hg38.knowngene=3.20.0
- bioconda::bioconductor-txdb.hsapiens.ucsc.hg19.knowngene=3.2.2
- conda-forge::r-optparse=1.7.5

16 changes: 7 additions & 9 deletions modules/nf-core/purecn/coverage/main.nf
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Expand Up @@ -6,8 +6,8 @@ process PURECN_COVERAGE {
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-582ac26068889091d5e798347c637f8208d77a71:a29c64a63498b1ee8b192521fdf6ed3c65506994-0':
'biocontainers/mulled-v2-582ac26068889091d5e798347c637f8208d77a71:a29c64a63498b1ee8b192521fdf6ed3c65506994-0' }"
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/92/926f2b12a939f84566b934f3fd6136d33137130ed6563f70c3edf6664cdcc5c0/data':
'community.wave.seqera.io/library/bioconductor-org.hs.eg.db_bioconductor-purecn_bioconductor-txdb.hsapiens.ucsc.hg19.knowngene_bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_r-optparse:53ad9839eb9a0de2' }"

input:
tuple val(meta), path(bam), path(bai)
Expand All @@ -26,7 +26,6 @@ process PURECN_COVERAGE {

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def VERSION = '2.4.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.

if (task.stageInMode != 'link') {
Expand All @@ -49,20 +48,19 @@ process PURECN_COVERAGE {
"""

stub:

def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def png = args.contains("--skip-gc-norm") ? "" : "touch ${prefix}.png"
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def png = args.contains("--skip-gc-norm") ? "" : "touch ${prefix}.png"
def loess_qc_txt = args.contains("--skip-gc-norm") ? "" : "touch ${prefix}_loess_qc.txt"
def loess_txt = args.contains("--skip-gc-norm") ? "" : "touch ${prefix}_loess.txt.gz"
def loess_txt = args.contains("--skip-gc-norm") ? "" : "echo | gzip > ${prefix}_loess.txt.gz"
def VERSION = '2.4.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.

if (task.stageInMode != 'link') {
error "purecn/coverage can not handle staging files with symlinks. Please change the stageInmode option to 'Link'"
}

"""
touch ${prefix}.txt
echo | gzip > ${prefix}.txt.gz
touch ${prefix}.bed
${png}
${loess_qc_txt}
Expand Down
92 changes: 92 additions & 0 deletions modules/nf-core/purecn/coverage/tests/main.nf.test
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@@ -0,0 +1,92 @@
nextflow_process {

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

tag "modules"
tag "modules_nfcore"
tag "purecn"
tag "purecn/coverage"
config './nextflow.config'

test("homo_sapiens - skip_gc") {
when {
params {
module_args = "--skip-gc-norm"
}
process {
"""
input[0] = [ [ id:'test' ],
file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/purecn/purecn_ex1.bam', checkIfExists: true),
file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/purecn/purecn_ex1.bam.bai', checkIfExists: true)
]
input[1] = file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/purecn/purecn_ex1_intervals.txt', checkIfExists: true)
"""
}
}

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

}

test("homo_sapiens - stub") {
options "-stub"

when {
params {
module_args = ""
}
process {
"""
input[0] = [ [ id:'test' ],
file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/purecn/purecn_ex1.bam', checkIfExists: true),
file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/purecn/purecn_ex1.bam.bai', checkIfExists: true)
]
input[1] = file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/purecn/purecn_ex1_intervals.txt', checkIfExists: true)
"""
}
}

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

}

test("homo_sapiens - skip_gc - stub") {
options "-stub"

when {
params {
module_args = "--skip-gc-norm"
}
process {
"""
input[0] = [ [ id:'test' ],
file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/purecn/purecn_ex1.bam', checkIfExists: true),
file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/purecn/purecn_ex1.bam.bai', checkIfExists: true)
]
input[1] = file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/purecn/purecn_ex1_intervals.txt', checkIfExists: true)
"""
}
}

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

}

}
191 changes: 191 additions & 0 deletions modules/nf-core/purecn/coverage/tests/main.nf.test.snap
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@@ -0,0 +1,191 @@
{
"homo_sapiens - stub": {
"content": [
{
"0": [
[
{
"id": "test"
},
[
"test.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
"test_loess.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
]
],
"1": [
[
{
"id": "test"
},
"test.png:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"2": [
[
{
"id": "test"
},
"test_loess_qc.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"3": [
[
{
"id": "test"
},
"test_loess.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"4": [
"versions.yml:md5,96bf7ac8a6dce08c678dc1fc2cb89d66"
],
"loess_qc_txt": [
[
{
"id": "test"
},
"test_loess_qc.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"loess_txt": [
[
{
"id": "test"
},
"test_loess.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"png": [
[
{
"id": "test"
},
"test.png:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"txt": [
[
{
"id": "test"
},
[
"test.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
"test_loess.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
]
],
"versions": [
"versions.yml:md5,96bf7ac8a6dce08c678dc1fc2cb89d66"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-03-07T20:17:01.199920116"
},
"homo_sapiens - skip_gc - stub": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"1": [

],
"2": [

],
"3": [

],
"4": [
"versions.yml:md5,96bf7ac8a6dce08c678dc1fc2cb89d66"
],
"loess_qc_txt": [

],
"loess_txt": [

],
"png": [

],
"txt": [
[
{
"id": "test"
},
"test.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"versions": [
"versions.yml:md5,96bf7ac8a6dce08c678dc1fc2cb89d66"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-03-07T20:17:11.624889158"
},
"homo_sapiens - skip_gc": {
"content": [
{
"0": [
[
{
"id": "test"
},
"purecn_ex1_coverage.txt.gz:md5,fd82ba1e942aeef3e07d5565cf80bd37"
]
],
"1": [

],
"2": [

],
"3": [

],
"4": [
"versions.yml:md5,96bf7ac8a6dce08c678dc1fc2cb89d66"
],
"loess_qc_txt": [

],
"loess_txt": [

],
"png": [

],
"txt": [
[
{
"id": "test"
},
"purecn_ex1_coverage.txt.gz:md5,fd82ba1e942aeef3e07d5565cf80bd37"
]
],
"versions": [
"versions.yml:md5,96bf7ac8a6dce08c678dc1fc2cb89d66"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-03-07T20:16:50.672409307"
}
}
5 changes: 5 additions & 0 deletions modules/nf-core/purecn/coverage/tests/nextflow.config
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@@ -0,0 +1,5 @@
process {
withName: PURECN_COVERAGE {
ext.args = params.module_args
}
}
3 changes: 0 additions & 3 deletions tests/config/pytest_modules.yml
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Expand Up @@ -311,9 +311,6 @@ pretextsnapshot:
propr/logratio:
- modules/nf-core/propr/logratio/**
- tests/modules/nf-core/propr/logratio/**
purecn/coverage:
- modules/nf-core/purecn/coverage/**
- tests/modules/nf-core/purecn/coverage/**
purecn/run:
- modules/nf-core/purecn/run/**
- tests/modules/nf-core/purecn/run/**
Expand Down
18 changes: 0 additions & 18 deletions tests/modules/nf-core/purecn/coverage/main.nf
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8 changes: 0 additions & 8 deletions tests/modules/nf-core/purecn/coverage/nextflow.config
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10 changes: 0 additions & 10 deletions tests/modules/nf-core/purecn/coverage/test.yml
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