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Added nf-tests to gprofile2/gost
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@nschcolnicov
nschcolnicov committed Dec 27, 2024
1 parent 51c2192 commit 8aa0e56
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Showing 5 changed files with 334 additions and 3 deletions.
24 changes: 22 additions & 2 deletions modules/nf-core/gprofiler2/gost/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process GPROFILER2_GOST {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-3712554873398d849d0d11b22440f41febbc4ede:aa19bb8afc0ec6456a4f3cd650f7577c3bbdd4f3-0':
'biocontainers/mulled-v2-3712554873398d849d0d11b22440f41febbc4ede:aa19bb8afc0ec6456a4f3cd650f7577c3bbdd4f3-0' }"
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e4/e4b0e10a72db4ad519c128c4e3cef6e10bc1a83440af31f105ab389a5532589a/data':
'community.wave.seqera.io/library/r-ggplot2_r-gprofiler2:fab855ea9f680400' }"

input:
tuple val(meta), path(de_file)
Expand All @@ -28,4 +28,24 @@ process GPROFILER2_GOST {

script:
template 'gprofiler2_gost.R'

stub:
def prefix = task.ext.prefix ?: meta.id
"""
touch ${prefix}.gprofiler2.all_enriched_pathways.tsv
touch ${prefix}.gprofiler2.gost_results.rds
touch ${prefix}.gprofiler2.gostplot.png
touch ${prefix}.gprofiler2.gostplot.html
touch ${prefix}.gprofiler2.*.sub_enriched_pathways.tsv
touch ${prefix}.gprofiler2.*.sub_enriched_pathways.png
touch ${prefix}.ENSG_filtered.gmt
touch ${prefix}.R_sessionInfo.log
cat <<-END_VERSIONS > versions.yml
"${task.process}":
r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
r-ggplot2: \$(Rscript -e "library(ggplot2); cat(as.character(packageVersion('ggplot2')))")
r-gprofiler2: \$(Rscript -e "library(gprofiler2); cat(as.character(packageVersion('gprofiler2')))")
END_VERSIONS
"""
}
2 changes: 1 addition & 1 deletion modules/nf-core/gprofiler2/gost/templates/gprofiler2_gost.R
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Original file line number Diff line number Diff line change
Expand Up @@ -449,7 +449,7 @@ gprofiler2.version <- as.character(packageVersion('gprofiler2'))
ggplot2.version <- as.character(packageVersion('ggplot2'))
writeLines(
c(
'"\${task.process}":',
'"$task.process":',
paste(' r-base:', r.version),
paste(' r-ggplot2:', ggplot2.version),
paste(' r-gprofiler2:', gprofiler2.version)
Expand Down
115 changes: 115 additions & 0 deletions modules/nf-core/gprofiler2/gost/tests/main.nf.test
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Original file line number Diff line number Diff line change
@@ -0,0 +1,115 @@
nextflow_process {

name "Test Process GPROFILER2_GOST"
script "../main.nf"
process "GPROFILER2_GOST"
config "./nextflow.config"

tag "modules"
tag "modules_nfcore"
tag "gprofiler"
tag "gprofiler_gost"
tag "gost"
tag "gprofiler2/gost"
tag "gprofiler2"

test("test") {

when {
params{
gprofiler2_significant = true
gprofiler2_measure_underrepresentation = false
gprofiler2_correction_method = "gSCS"
gprofiler2_evcodes = false
gprofiler2_max_qval = 0.05
gprofiler2_domain_scope = "annotated"
gprofiler2_min_diff = 1
report_round_digits = 4
gprofiler2_palette_name = "Blues"
differential_feature_id_column = "gene_id"
gprofiler2_token = null
gprofiler2_organism = "mmusculus"
gprofiler2_background_column = null
gprofiler2_sources = null

module_args = [
"--significant \"${params.gprofiler2_significant}\"",
"--measure_underrepresentation \"${params.gprofiler2_measure_underrepresentation}\"",
"--correction_method \"${params.gprofiler2_correction_method}\"",
"--evcodes \"${params.gprofiler2_evcodes}\"",
"--pval_threshold \"${params.gprofiler2_max_qval}\"",
"--domain_scope ${params.gprofiler2_domain_scope}",
"--min_diff \"${params.gprofiler2_min_diff}\"",
"--round_digits ${params.report_round_digits}",
"--palette_name \"${params.gprofiler2_palette_name}\"",
((params.differential_feature_id_column == null) ? '' : "--de_id_column \"${params.differential_feature_id_column}\""),
((params.gprofiler2_token == null) ? '' : "--token \"${params.gprofiler2_token}\""),
((params.gprofiler2_organism == null) ? '' : "--organism \"${params.gprofiler2_organism}\""),
((params.gprofiler2_background_column == null) ? '' : "--background_column \"${params.gprofiler2_background_column}\""),
((params.gprofiler2_sources == null) ? '' : "--sources \"${params.gprofiler2_sources}\"")
].join(' ').trim()
}
process {
"""
input[0] = [['id':'Condition_genotype_WT_KO', 'variable':'Condition genotype', 'reference':'WT', 'target':'KO', 'blocking':'batch'], file("https://github.com/nf-core/test-datasets/raw/refs/heads/differentialabundance/modules_testdata/Condition_genotype_WT_KO.deseq2.results_filtered.tsv", checkIfExists: true)]
input[1] = file("https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/mus_musculus/gene_set_analysis/mh.all.v2022.1.Mm.symbols.gmt", checkIfExists: true)
input[2] = file("https://github.com/nf-core/test-datasets/raw/refs/heads/differentialabundance/modules_testdata/study.filtered.tsv", checkIfExists: true)
"""
}
}

then {
assertAll (
{ assert process.success },
{ assert snapshot(
process.out.all_enrich,
process.out.plot_png,
process.out.sub_enrich,
process.out.sub_plot,
process.out.filtered_gmt,
process.out.session_info,
process.out.versions,
process.out.plot_html.collect{ meta,html -> file(html).name }, //assert unstable file
process.out.rds.collect{ meta,rds -> file(rds).name } //assert unstable file
).match()
}
)
}
}

test("stub") {

options "-stub"

when {
params{
module_args = null
}
process {
"""
input[0] = [['id':'Condition_genotype_WT_KO', 'variable':'Condition genotype', 'reference':'WT', 'target':'KO', 'blocking':'batch'], file("https://github.com/nf-core/test-datasets/raw/refs/heads/differentialabundance/modules_testdata/Condition_genotype_WT_KO.deseq2.results_filtered.tsv", checkIfExists: true)]
input[1] = file("https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/mus_musculus/gene_set_analysis/mh.all.v2022.1.Mm.symbols.gmt", checkIfExists: true)
input[2] = file("https://github.com/nf-core/test-datasets/raw/refs/heads/differentialabundance/modules_testdata/study.filtered.tsv", checkIfExists: true)
"""
}
}

then {
assertAll (
{ assert process.success },
{ assert snapshot(
process.out.all_enrich,
process.out.plot_png,
process.out.sub_enrich,
process.out.sub_plot,
process.out.filtered_gmt,
process.out.session_info,
process.out.versions,
process.out.plot_html.collect{ meta,html -> file(html).name }, //assert unstable file
process.out.rds.collect{ meta,rds -> file(rds).name } //assert unstable file
).match()
}
)
}
}
}
193 changes: 193 additions & 0 deletions modules/nf-core/gprofiler2/gost/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -0,0 +1,193 @@
{
"test": {
"content": [
[
[
{
"id": "Condition_genotype_WT_KO",
"variable": "Condition genotype",
"reference": "WT",
"target": "KO",
"blocking": "batch"
},
"Condition_genotype_WT_KO.gprofiler2.all_enriched_pathways.tsv:md5,1134a02ca061c463bcbff277eefbfb19"
]
],
[
[
{
"id": "Condition_genotype_WT_KO",
"variable": "Condition genotype",
"reference": "WT",
"target": "KO",
"blocking": "batch"
},
"Condition_genotype_WT_KO.gprofiler2.gostplot.png:md5,4b83d1bcf7dc9dbf6cef3d545e440c5b"
]
],
[
[
{
"id": "Condition_genotype_WT_KO",
"variable": "Condition genotype",
"reference": "WT",
"target": "KO",
"blocking": "batch"
},
[
"Condition_genotype_WT_KO.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,d527b94cdb160070bcaa0bfb0cecf914",
"Condition_genotype_WT_KO.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,ef418c3f06d50446317928e37ec8ddfb",
"Condition_genotype_WT_KO.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,e460d4917feb0b64d334a528f59e0731",
"Condition_genotype_WT_KO.gprofiler2.HP.sub_enriched_pathways.tsv:md5,865d8f092503552831c51d775a98c6eb",
"Condition_genotype_WT_KO.gprofiler2.KEGG.sub_enriched_pathways.tsv:md5,413724002abe683f376ea914d4f21ade",
"Condition_genotype_WT_KO.gprofiler2.MIRNA.sub_enriched_pathways.tsv:md5,fce81051d7af955ddb2925ba2da9ff57",
"Condition_genotype_WT_KO.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,e89e1876698ea644671a0720c85f4dbb",
"Condition_genotype_WT_KO.gprofiler2.TF.sub_enriched_pathways.tsv:md5,e272217ec7fcf01ea463ab8bcc8335cf",
"Condition_genotype_WT_KO.gprofiler2.WP.sub_enriched_pathways.tsv:md5,fdd1efa836d85bb127e933e925290cba"
]
]
],
[
[
{
"id": "Condition_genotype_WT_KO",
"variable": "Condition genotype",
"reference": "WT",
"target": "KO",
"blocking": "batch"
},
[
"Condition_genotype_WT_KO.gprofiler2.GO:BP.sub_enriched_pathways.png:md5,d89498267e985adf0ad1266e2deb9f48",
"Condition_genotype_WT_KO.gprofiler2.GO:CC.sub_enriched_pathways.png:md5,e04cdd51b200671613254d021d3af242",
"Condition_genotype_WT_KO.gprofiler2.GO:MF.sub_enriched_pathways.png:md5,33ea0652d78111978677acde0fe7f807",
"Condition_genotype_WT_KO.gprofiler2.HP.sub_enriched_pathways.png:md5,6c040ac4baba73ae5637b00650e6aea1",
"Condition_genotype_WT_KO.gprofiler2.KEGG.sub_enriched_pathways.png:md5,fbd232c4eeced95ceda60b43a02dbe1f",
"Condition_genotype_WT_KO.gprofiler2.MIRNA.sub_enriched_pathways.png:md5,956880d3bf4852a06b0ffaaaba565732",
"Condition_genotype_WT_KO.gprofiler2.REAC.sub_enriched_pathways.png:md5,0e8f9217d275668986771dc7fede3170",
"Condition_genotype_WT_KO.gprofiler2.TF.sub_enriched_pathways.png:md5,0697164bc87e95e6508db966df94e01e",
"Condition_genotype_WT_KO.gprofiler2.WP.sub_enriched_pathways.png:md5,09976762c7541ff9e5009e8763986845"
]
]
],
[

],
[
[
{
"id": "Condition_genotype_WT_KO",
"variable": "Condition genotype",
"reference": "WT",
"target": "KO",
"blocking": "batch"
},
"R_sessionInfo.log:md5,47643dc530c1a01102cc9db58c1f6b62"
]
],
[
"versions.yml:md5,7ff4ab78463faf97bba7e698ed9a9069"
],
[
"Condition_genotype_WT_KO.gprofiler2.gostplot.html"
],
[
"Condition_genotype_WT_KO.gprofiler2.gost_results.rds"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2024-12-27T19:16:24.14894842"
},
"stub": {
"content": [
[
[
{
"id": "Condition_genotype_WT_KO",
"variable": "Condition genotype",
"reference": "WT",
"target": "KO",
"blocking": "batch"
},
"Condition_genotype_WT_KO.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
[
[
{
"id": "Condition_genotype_WT_KO",
"variable": "Condition genotype",
"reference": "WT",
"target": "KO",
"blocking": "batch"
},
"Condition_genotype_WT_KO.gprofiler2.gostplot.png:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
[
[
{
"id": "Condition_genotype_WT_KO",
"variable": "Condition genotype",
"reference": "WT",
"target": "KO",
"blocking": "batch"
},
"Condition_genotype_WT_KO.gprofiler2.*.sub_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
[
[
{
"id": "Condition_genotype_WT_KO",
"variable": "Condition genotype",
"reference": "WT",
"target": "KO",
"blocking": "batch"
},
"Condition_genotype_WT_KO.gprofiler2.*.sub_enriched_pathways.png:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
[
[
{
"id": "Condition_genotype_WT_KO",
"variable": "Condition genotype",
"reference": "WT",
"target": "KO",
"blocking": "batch"
},
"Condition_genotype_WT_KO.ENSG_filtered.gmt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
[
[
{
"id": "Condition_genotype_WT_KO",
"variable": "Condition genotype",
"reference": "WT",
"target": "KO",
"blocking": "batch"
},
"Condition_genotype_WT_KO.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
[
"versions.yml:md5,7ff4ab78463faf97bba7e698ed9a9069"
],
[
"Condition_genotype_WT_KO.gprofiler2.gostplot.html"
],
[
"Condition_genotype_WT_KO.gprofiler2.gost_results.rds"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2024-12-27T19:16:37.689819563"
}
}
3 changes: 3 additions & 0 deletions modules/nf-core/gprofiler2/gost/tests/nextflow.config
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Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
process {
ext.args = params.module_args
}

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