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Migrate umitools/group to nf-test #6653

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merged 11 commits into from
Nov 20, 2024
Merged

Migrate umitools/group to nf-test #6653

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5e5350a
Swap umitools/group to nf-test
SPPearce Sep 16, 2024
3483153
Update tests and meta
SPPearce Sep 17, 2024
a1fa1eb
Merge branch 'master' into umitools_nftest
SPPearce Sep 17, 2024
faec929
Merge branch 'master' into umitools_nftest
SPPearce Sep 17, 2024
e426c9e
Merge branch 'master' into umitools_nftest
SPPearce Nov 5, 2024
a72b3ff
Apply suggestions from code review
SPPearce Nov 5, 2024
a3a97ba
Merge branch 'master' into umitools_nftest
SPPearce Nov 19, 2024
10ea39a
Merge branch 'master' into umitools_nftest
SPPearce Nov 20, 2024
cce72a8
Update snapshot
SPPearce Nov 20, 2024
7d4c77d
Merge branch 'master' into umitools_nftest
Joon-Klaps Nov 20, 2024
a01bfcb
Merge branch 'master' into umitools_nftest
Joon-Klaps Nov 20, 2024
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7 changes: 4 additions & 3 deletions modules/nf-core/umitools/group/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ process UMITOOLS_GROUP {

script:
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
prefix = task.ext.prefix ?: "${meta.id}_grouped"
def paired = meta.single_end ? "" : "--paired"
output_bam = create_bam ? "--output-bam -S ${prefix}.bam" : ""
group_info = get_group_info ? "--group-out ${prefix}.tsv" : ""
Expand All @@ -48,11 +48,12 @@ process UMITOOLS_GROUP {
"""

stub:
prefix = task.ext.prefix ?: "${meta.id}"
prefix = task.ext.prefix ?: "${meta.id}_grouped"
output_bam = create_bam ? "touch ${prefix}.bam" : ""
"""
touch ${prefix}.bam
touch ${prefix}.log
touch ${prefix}.tsv
$output_bam

cat <<-END_VERSIONS > versions.yml
"${task.process}":
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169 changes: 169 additions & 0 deletions modules/nf-core/umitools/group/tests/main.nf.test
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Original file line number Diff line number Diff line change
@@ -0,0 +1,169 @@
nextflow_process {

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

tag "modules"
tag "modules_nfcore"
tag "umitools"
tag "umitools/extract"
tag "umitools/group"
tag "bwa/index"
tag "bwa/mem"
tag "samtools/index"

setup {
run("UMITOOLS_EXTRACT") {
script "../../extract/main.nf"
config "./nextflow.config"
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
]
]
"""
}
}

run("BWA_INDEX") {
script "../../../bwa/index/main.nf"
process {
"""
input[0] = [
[ id:'sarscov2'],
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]
"""
}
}

run("BWA_MEM") {
script "../../../bwa/mem/main.nf"
process {
"""
input[0] = UMITOOLS_EXTRACT.out.reads
input[1] = BWA_INDEX.out.index
input[2] = [ [], [] ]
input[3] = true
"""
}
}

run("SAMTOOLS_INDEX") {
script "../../../samtools/index/main.nf"
process {
"""
input[0] = BWA_MEM.out.bam
"""
}
}

}

test("no_umi") {

when {
process {
"""
input[0] = [[ id:'test'], // meta map
file(params.test_data_base + '/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
file(params.test_data_base + '/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
]
input[1] = true
input[2] = true
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
bam(process.out.bam[0][1]).getReadsMD5(),
process.out.tsv,
file(process.out.log[0][1]).readLines()[0..1],
process.out.versions
).match() }
)
}

}

test("with_umi - create only bam") {

when {
process {
"""
input[0] = BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0])
input[1] = true
input[2] = false
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
bam(process.out.bam[0][1]).getReadsMD5(),
file(process.out.log[0][1]).readLines()[0..1],
process.out.versions
).match() }
)
}

}

test("with_umi - create bam and tsv") {

when {
process {
"""
input[0] = BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0])
input[1] = true
input[2] = true
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.tsv,
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bam(process.out.bam[0][1]).getReadsMD5(),
file(process.out.log[0][1]).readLines()[0..1],
process.out.versions
).match() }
)
}

}

test("with_umi - stub") {
options "-stub"
when {
process {
"""
input[0] = BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0])
input[1] = true
input[2] = true
"""
}
}

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

}

}
141 changes: 141 additions & 0 deletions modules/nf-core/umitools/group/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -0,0 +1,141 @@
{
"with_umi - create only bam": {
"content": [
"72da540b9a840cf39e3567cc35045143",
[
"# UMI-tools version: 1.1.5",
"# output generated by group -I test.bam --output-bam -S test_grouped.bam -L test_grouped.log --paired --random-seed=100"
],
[
"versions.yml:md5,1f4cec69f12f1759748ed167701b321c"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.1"
},
"timestamp": "2024-11-20T13:51:08.650455694"
},
"with_umi - stub": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
"test_grouped.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
[
{
"id": "test",
"single_end": false
},
"test_grouped.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"2": [
[
{
"id": "test",
"single_end": false
},
"test_grouped.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"3": [
"versions.yml:md5,1f4cec69f12f1759748ed167701b321c"
],
"bam": [
[
{
"id": "test",
"single_end": false
},
"test_grouped.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"log": [
[
{
"id": "test",
"single_end": false
},
"test_grouped.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"tsv": [
[
{
"id": "test",
"single_end": false
},
"test_grouped.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,1f4cec69f12f1759748ed167701b321c"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-16T19:52:11.292296043"
},
"no_umi": {
"content": [
"b01829d27fad55e707745f86311b443e",
[
[
{
"id": "test"
},
"test_grouped.tsv:md5,1a3ccdc00df59fa89c79ad482980a003"
]
],
[
"# UMI-tools version: 1.1.5",
"# output generated by group -I test.paired_end.sorted.bam --output-bam -S test_grouped.bam -L test_grouped.log --group-out test_grouped.tsv --paired --random-seed=100"
],
[
"versions.yml:md5,1f4cec69f12f1759748ed167701b321c"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-17T07:22:24.041871851"
},
"with_umi - create bam and tsv": {
"content": [
[
[
{
"id": "test",
"single_end": false
},
"test_grouped.tsv:md5,d652eb6570057e9e709e8cac5f43d00c"
]
],
"72da540b9a840cf39e3567cc35045143",
[
"# UMI-tools version: 1.1.5",
"# output generated by group -I test.bam --output-bam -S test_grouped.bam -L test_grouped.log --group-out test_grouped.tsv --paired --random-seed=100"
],
[
"versions.yml:md5,1f4cec69f12f1759748ed167701b321c"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.1"
},
"timestamp": "2024-11-20T13:51:34.459633546"
}
}
5 changes: 5 additions & 0 deletions modules/nf-core/umitools/group/tests/nextflow.config
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Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
process {
withName: UMITOOLS_EXTRACT {
ext.args = '--bc-pattern="NNNN"'
}
}
3 changes: 0 additions & 3 deletions tests/config/pytest_modules.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -696,9 +696,6 @@ ultra/index:
ultra/pipeline:
- modules/nf-core/ultra/pipeline/**
- tests/modules/nf-core/ultra/pipeline/**
umitools/group:
- modules/nf-core/umitools/group/**
- tests/modules/nf-core/umitools/group/**
universc:
- modules/nf-core/universc/**
- tests/modules/nf-core/universc/**
Expand Down
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