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add stub for local modules #1331

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merged 5 commits into from
Jul 2, 2024
Merged

add stub for local modules #1331

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858cd5d
add stub for local/deseq2_qc
maxulysse Jun 21, 2024
451483b
add stubs for all + test for most
maxulysse Jun 21, 2024
7af2a7f
Update CHANGELOG.md
maxulysse Jul 2, 2024
fa2f92b
Merge branch 'dev' into dev
maxulysse Jul 2, 2024
7e9077e
update snaps
maxulysse Jul 2, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -96,6 +96,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
- [PR #1328](https://github.com/nf-core/rnaseq/pull/1328) - Add pipeline level test for STAR-RSEM and HISAT2
- [PR #1329](https://github.com/nf-core/rnaseq/pull/1329) - Remove tags from all nf-test files
- [PR #1330](https://github.com/nf-core/rnaseq/pull/1330) - Update all nf-core/modules and subworkflows
- [PR #1331](https://github.com/nf-core/rnaseq/pull/1331) - Adding stubs for local modules

### Parameters

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27 changes: 27 additions & 0 deletions modules/local/deseq2_qc/main.nf
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Expand Up @@ -57,4 +57,31 @@ process DESEQ2_QC {
bioconductor-deseq2: \$(Rscript -e "library(DESeq2); cat(as.character(packageVersion('DESeq2')))")
END_VERSIONS
"""

stub:
def args2 = task.ext.args2 ?: ''
def label_lower = args2.toLowerCase()
prefix = task.ext.prefix ?: "deseq2"
"""
mkdir size_factors
touch ${label_lower}.pca.vals_mqc.tsv
touch ${label_lower}.sample.dists_mqc.tsv
touch ${prefix}.plots.pdf
touch ${prefix}.dds.RData
touch ${prefix}.pca.vals.txt
touch ${prefix}.sample.dists.txt
touch R_sessionInfo.log
touch size_factors/${prefix}.size_factors.RData

for i in `head $counts -n 1 | cut -f3-`;
do
touch size_factors/\${i}.size_factors.RData
done
Comment on lines +76 to +79
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I'm quite proud of that one


cat <<-END_VERSIONS > versions.yml
"${task.process}":
r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
bioconductor-deseq2: \$(Rscript -e "library(DESeq2); cat(as.character(packageVersion('DESeq2')))")
END_VERSIONS
"""
}
25 changes: 23 additions & 2 deletions modules/local/deseq2_qc/tests/main.nf.test
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Expand Up @@ -26,11 +26,32 @@ nextflow_process {
process.out.pca_multiqc,
process.out.pca_txt,
process.out.rdata,
process.out.size_factors
process.out.size_factors,
process.out.versions
).match() }
)
}

}

test("parse count data correctly - stub") {

options "-stub"

when {
process {
"""
input[0] = file(params.pipelines_testdata_base_path + "deseq2qc/countFile.tsv", checkIfExists: true)
input[1] = file(params.pipelines_testdata_base_path + "deseq2qc/deseq2_pca_header.txt", checkIfExists: true)
input[2] = file(params.pipelines_testdata_base_path + "deseq2qc/deseq2_clustering_header.txt", checkIfExists: true)
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}
}
92 changes: 87 additions & 5 deletions modules/local/deseq2_qc/tests/main.nf.test.snap
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@@ -1,8 +1,87 @@
{
"parse count data correctly - stub": {
"content": [
{
"0": [
"deseq2.plots.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"1": [
"deseq2.dds.RData:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"2": [
"deseq2.pca.vals.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"3": [

],
"4": [
"deseq2.sample.dists.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"5": [

],
"6": [
"R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"7": [
[
"RAP1_IAA_30M_REP1.size_factors.RData:md5,d41d8cd98f00b204e9800998ecf8427e",
"RAP1_UNINDUCED_REP1.size_factors.RData:md5,d41d8cd98f00b204e9800998ecf8427e",
"RAP1_UNINDUCED_REP2.size_factors.RData:md5,d41d8cd98f00b204e9800998ecf8427e",
"WT_REP1.size_factors.RData:md5,d41d8cd98f00b204e9800998ecf8427e",
"WT_REP2.size_factors.RData:md5,d41d8cd98f00b204e9800998ecf8427e",
"deseq2.size_factors.RData:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"8": [
"versions.yml:md5,60f8e4f473397a4b5d1a3dc490c93ec5"
],
"dists_multiqc": [

],
"dists_txt": [
"deseq2.sample.dists.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"log": [
"R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"pca_multiqc": [

],
"pca_txt": [
"deseq2.pca.vals.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"pdf": [
"deseq2.plots.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"rdata": [
"deseq2.dds.RData:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"size_factors": [
[
"RAP1_IAA_30M_REP1.size_factors.RData:md5,d41d8cd98f00b204e9800998ecf8427e",
"RAP1_UNINDUCED_REP1.size_factors.RData:md5,d41d8cd98f00b204e9800998ecf8427e",
"RAP1_UNINDUCED_REP2.size_factors.RData:md5,d41d8cd98f00b204e9800998ecf8427e",
"WT_REP1.size_factors.RData:md5,d41d8cd98f00b204e9800998ecf8427e",
"WT_REP2.size_factors.RData:md5,d41d8cd98f00b204e9800998ecf8427e",
"deseq2.size_factors.RData:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,60f8e4f473397a4b5d1a3dc490c93ec5"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-06-21T11:38:08.92794"
},
"parse count data correctly": {
"content": [
[

],
[
"deseq2.sample.dists.txt:md5,1616ce40eb58ee75640efed219c6bbec"
Expand All @@ -11,7 +90,7 @@
"R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676"
],
[

],
[
"deseq2.pca.vals.txt:md5,4cda8e32ec39326c1350e77b4b607aad"
Expand All @@ -28,12 +107,15 @@
"WT_REP2.txt:md5,2ce093f2c2e92c1bde1cd3da91ac884c",
"deseq2.size_factors.RData:md5,51c6643a0f8a9edabbff8df0165451f2"
]
],
[
"versions.yml:md5,60f8e4f473397a4b5d1a3dc490c93ec5"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "24.04.2"
},
"timestamp": "2024-03-07T12:34:51.582179"
"timestamp": "2024-06-21T11:21:20.349616"
}
}
}
10 changes: 10 additions & 0 deletions modules/local/gtf2bed/main.nf
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Expand Up @@ -28,4 +28,14 @@ process GTF2BED {
perl: \$(echo \$(perl --version 2>&1) | sed 's/.*v\\(.*\\)) built.*/\\1/')
END_VERSIONS
"""

stub:
"""
touch ${gtf.baseName}.bed

cat <<-END_VERSIONS > versions.yml
"${task.process}":
perl: \$(echo \$(perl --version 2>&1) | sed 's/.*v\\(.*\\)) built.*/\\1/')
END_VERSIONS
"""
}
19 changes: 19 additions & 0 deletions modules/local/gtf2bed/tests/main.nf.test
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Expand Up @@ -20,6 +20,25 @@ nextflow_process {
{ assert snapshot(process.out).match() }
)
}
}

test("sarscov2 - bam - stub") {

options "-stub"

when {
process {
"""
input[0] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}
}
23 changes: 23 additions & 0 deletions modules/local/gtf2bed/tests/main.nf.test.snap
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@@ -1,4 +1,27 @@
{
"sarscov2 - bam - stub": {
"content": [
{
"0": [
"genome.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"1": [
"versions.yml:md5,d04d815c224b980b6f3818d4b2fd4fe3"
],
"bed": [
"genome.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"versions": [
"versions.yml:md5,d04d815c224b980b6f3818d4b2fd4fe3"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-06-21T11:46:28.123826"
},
"sarscov2 - bam": {
"content": [
{
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10 changes: 10 additions & 0 deletions modules/local/gtf_filter/main.nf
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Expand Up @@ -29,4 +29,14 @@ process GTF_FILTER {
python: \$(python --version | sed 's/Python //g')
END_VERSIONS
"""

stub:
"""
touch ${fasta.baseName}.filtered.gtf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
python: \$(python --version | sed 's/Python //g')
END_VERSIONS
"""
}
23 changes: 21 additions & 2 deletions modules/local/gtf_filter/tests/main.nf.test
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Expand Up @@ -4,7 +4,7 @@ nextflow_process {
script "../main.nf"
process "GTF_FILTER"

test("Should run without failures") {
test("sarscov2 - fasta - gtf") {

when {
process {
Expand All @@ -21,7 +21,26 @@ nextflow_process {
{ assert snapshot(process.out).match() }
)
}

}

test("sarscov2 - fasta - gtf - stub") {

options "-stub"

when {
process {
"""
input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}
}
29 changes: 26 additions & 3 deletions modules/local/gtf_filter/tests/main.nf.test.snap
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@@ -1,5 +1,5 @@
{
"Should run without failures": {
"sarscov2 - fasta - gtf": {
"content": [
{
"0": [
Expand All @@ -18,8 +18,31 @@
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "24.04.2"
},
"timestamp": "2024-03-06T15:52:37.977802"
"timestamp": "2024-06-21T11:47:56.314297"
},
"sarscov2 - fasta - gtf - stub": {
"content": [
{
"0": [
"genome.filtered.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"1": [
"versions.yml:md5,4adf55ec05d247fd6d253459bd80856f"
],
"genome_gtf": [
"genome.filtered.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"versions": [
"versions.yml:md5,4adf55ec05d247fd6d253459bd80856f"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-06-21T11:48:19.085835"
}
}
12 changes: 12 additions & 0 deletions modules/local/multiqc_custom_biotype/main.nf
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Expand Up @@ -33,4 +33,16 @@ process MULTIQC_CUSTOM_BIOTYPE {
python: \$(python --version | sed 's/Python //g')
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.biotype_counts_mqc.tsv
touch ${prefix}.biotype_counts_rrna_mqc.tsv

cat <<-END_VERSIONS > versions.yml
"${task.process}":
python: \$(python --version | sed 's/Python //g')
END_VERSIONS
"""
}
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