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add stub and stub test to chromap, change test names #5872

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merged 8 commits into from
Jun 24, 2024
Merged

add stub and stub test to chromap, change test names #5872

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7156b15
add stub and stub test to chromap, change test names
famosab Jun 24, 2024
d81f6a2
Merge branch 'master' into chromap-stub
famosab Jun 24, 2024
748c389
add stub and stub test to chromap, change test names
famosab Jun 24, 2024
3e54f19
Merged origin/chromap-stub into chromap-stub
famosab Jun 24, 2024
8d729fd
change setup
famosab Jun 24, 2024
c48e7ea
Merge branch 'master' into chromap-stub
famosab Jun 24, 2024
0e9fadb
move setup out of test
famosab Jun 24, 2024
712bd5e
move
famosab Jun 24, 2024
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15 changes: 15 additions & 0 deletions modules/nf-core/chromap/chromap/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -92,4 +92,19 @@ process CHROMAP_CHROMAP {
END_VERSIONS
"""
}

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
echo "" | gzip > ${prefix}.bed.gz
touch ${prefix}.bam
echo "" | gzip > ${prefix}.tagAlign.gz
echo "" | gzip > ${prefix}.pairs.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
chromap: \$(echo \$(chromap --version 2>&1))
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}
102 changes: 59 additions & 43 deletions modules/nf-core/chromap/chromap/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -10,22 +10,37 @@ nextflow_process {
tag "chromap/chromap"
tag "chromap/index"

test("test_chromap_chromap_single_end") {

setup {
run("CHROMAP_INDEX") {
script "../../index/main.nf"
process {
"""
input[0] = Channel.of([
[:], // meta map
[file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
])
"""
}
setup {

run("CHROMAP_INDEX") {
script "../../index/main.nf"
process {
"""
input[0] = Channel.of([
[:], // meta map
[file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
])
"""
}
}

run("CHROMAP_INDEX", alias: "CHROMAP_INDEX_STUB") {
options "-stub"
script "../../index/main.nf"
process {
"""
input[0] = Channel.of([
[:], // meta map
[file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
])
"""
}
}

}

test("sarscov2 - single_end") {

when {
process {
"""
Expand All @@ -51,21 +66,7 @@ nextflow_process {
}
}

test("test_chromap_chromap_paired_end") {

setup {
run("CHROMAP_INDEX") {
script "../../index/main.nf"
process {
"""
input[0] = Channel.of([
[:], // meta map
[file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
])
"""
}
}
}
test("sarscov2 - paired_end ") {

when {
process {
Expand Down Expand Up @@ -96,21 +97,7 @@ nextflow_process {
}


test("test_chromap_chromap_paired_bam") {

setup {
run("CHROMAP_INDEX") {
script "../../index/main.nf"
process {
"""
input[0] = Channel.of([
[:], // meta map
[file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
])
"""
}
}
}
test("sarscov2 - paired_end - bam") {

when {
config "./nextflow.config"
Expand Down Expand Up @@ -142,4 +129,33 @@ nextflow_process {
}

}

test("sarscov2 - single_end - stub") {

options "-stub"

when {
process {
"""
input[0] = Channel.of([
[ id:'test', single_end:true ], // meta map
[file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)]
])
input[1] = Channel.of([[:], [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]])
input[2] = CHROMAP_INDEX_STUB.out.index
input[3] = []
input[4] = []
input[5] = []
input[6] = []
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}
}
137 changes: 113 additions & 24 deletions modules/nf-core/chromap/chromap/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,5 +1,58 @@
{
"test_chromap_chromap_paired_end": {
"sarscov2 - single_end": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": true
},
"test.bed.gz:md5,c45f5bb1c6eb56359760ce3827bfe3f4"
]
],
"1": [

],
"2": [

],
"3": [

],
"4": [
"versions.yml:md5,80647c2956e504334ad25ce31d33b539"
],
"bam": [

],
"bed": [
[
{
"id": "test",
"single_end": true
},
"test.bed.gz:md5,c45f5bb1c6eb56359760ce3827bfe3f4"
]
],
"pairs": [

],
"tagAlign": [

],
"versions": [
"versions.yml:md5,80647c2956e504334ad25ce31d33b539"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-06-24T09:14:34.016756"
},
"sarscov2 - paired_end ": {
"content": [
{
"0": [
Expand Down Expand Up @@ -48,21 +101,23 @@
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.1"
"nextflow": "24.04.2"
},
"timestamp": "2024-05-22T19:08:55.497043"
"timestamp": "2024-06-24T09:18:23.379305"
},
"test_chromap_chromap_paired_bam": {
"versions": {
"content": [
"test.bam"
[
"versions.yml:md5,80647c2956e504334ad25ce31d33b539"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.1"
},
"timestamp": "2024-05-22T19:09:02.957218"
"timestamp": "2024-05-22T19:09:02.94685"
},
"test_chromap_chromap_single_end": {
"sarscov2 - single_end - stub": {
"content": [
{
"0": [
Expand All @@ -71,38 +126,74 @@
"id": "test",
"single_end": true
},
"test.bed.gz:md5,c45f5bb1c6eb56359760ce3827bfe3f4"
"test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"1": [

[
{
"id": "test",
"single_end": true
},
"test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"2": [

[
{
"id": "test",
"single_end": true
},
"test.tagAlign.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"3": [

[
{
"id": "test",
"single_end": true
},
"test.pairs.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"4": [
"versions.yml:md5,80647c2956e504334ad25ce31d33b539"
],
"bam": [

[
{
"id": "test",
"single_end": true
},
"test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"bed": [
[
{
"id": "test",
"single_end": true
},
"test.bed.gz:md5,c45f5bb1c6eb56359760ce3827bfe3f4"
"test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"pairs": [

[
{
"id": "test",
"single_end": true
},
"test.pairs.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"tagAlign": [

[
{
"id": "test",
"single_end": true
},
"test.tagAlign.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"versions": [
"versions.yml:md5,80647c2956e504334ad25ce31d33b539"
Expand All @@ -111,20 +202,18 @@
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.1"
"nextflow": "24.04.2"
},
"timestamp": "2024-05-22T19:08:47.822066"
"timestamp": "2024-06-24T09:14:51.782404"
},
"versions": {
"sarscov2 - paired_end - bam": {
"content": [
[
"versions.yml:md5,80647c2956e504334ad25ce31d33b539"
]
"test.bam"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.1"
"nextflow": "24.04.2"
},
"timestamp": "2024-05-22T19:09:02.94685"
"timestamp": "2024-06-24T09:14:46.389216"
}
}
}
11 changes: 11 additions & 0 deletions modules/nf-core/chromap/index/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -33,4 +33,15 @@ process CHROMAP_INDEX {
chromap: \$(echo \$(chromap --version 2>&1))
END_VERSIONS
"""

stub:
def prefix = fasta.baseName
"""
touch ${prefix}.index

cat <<-END_VERSIONS > versions.yml
"${task.process}":
chromap: \$(echo \$(chromap --version 2>&1))
END_VERSIONS
"""
}
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