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Added nftests to gseagsea #7266

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merged 14 commits into from
Jan 13, 2025
Merged

Added nftests to gseagsea #7266

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d4edce2
Added nftests to gseagsea
nschcolnicov Dec 31, 2024
448f25e
Update input files
nschcolnicov Dec 31, 2024
8715073
fix nftests
nschcolnicov Jan 2, 2025
f283cf5
Merge branch 'master' into add_nftests_gseagsea
SPPearce Jan 7, 2025
4309064
Address PR comments
nschcolnicov Jan 8, 2025
73c623a
Merge branch 'add_nftests_gseagsea' of https://github.com/nf-core/mod…
nschcolnicov Jan 8, 2025
12c7fb7
Add seed setting parameter for stabilizing results
nschcolnicov Jan 9, 2025
f122ff2
Merge branch 'master' into add_nftests_gseagsea
nschcolnicov Jan 9, 2025
6cf8728
Fix linting
nschcolnicov Jan 9, 2025
eba45cb
Merge branch 'master' into add_nftests_gseagsea
SPPearce Jan 10, 2025
230f182
Merge branch 'master' of https://github.com/nf-core/modules into add_…
nschcolnicov Jan 13, 2025
d1de0bf
Add default random seed
nschcolnicov Jan 13, 2025
6a19acd
Merge branch 'add_nftests_gseagsea' of https://github.com/nf-core/mod…
nschcolnicov Jan 13, 2025
ff01cfc
Update datasets paths
nschcolnicov Jan 13, 2025
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80 changes: 51 additions & 29 deletions modules/nf-core/gsea/gsea/main.nf
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Expand Up @@ -4,51 +4,48 @@ process GSEA_GSEA {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gsea:4.3.2--hdfd78af_0':
'biocontainers/gsea:4.3.2--hdfd78af_0' }"
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0f/0f4fe28961396eeeaa98484cb4f2db5c79abfdf117700df132312fe5c41bff81/data':
'community.wave.seqera.io/library/gsea:4.3.2--a7421d7504fd7c81' }"

input:
tuple val(meta), path(gct), path(cls), path(gene_sets)
tuple val(reference), val(target)
path(chip) // Optional identifier mapping file

output:
tuple val(meta), path("*.rpt") , emit: rpt
tuple val(meta), path("*index.html") , emit: index_html
tuple val(meta), path("*heat_map_corr_plot.html") , emit: heat_map_corr_plot
tuple val(meta), path("*gsea_report_for_${reference}.tsv") , emit: report_tsvs_ref
tuple val(meta), path("*gsea_report_for_${reference}.html"), emit: report_htmls_ref
tuple val(meta), path("*gsea_report_for_${target}.tsv") , emit: report_tsvs_target
tuple val(meta), path("*gsea_report_for_${target}.html") , emit: report_htmls_target
tuple val(meta), path("*ranked_gene_list*.tsv") , emit: ranked_gene_list
tuple val(meta), path("*gene_set_sizes.tsv") , emit: gene_set_sizes
tuple val(meta), path("*global_es_histogram.png") , emit: histogram
tuple val(meta), path("*heat_map_1.png") , emit: heatmap
tuple val(meta), path("*pvalues_vs_nes_plot.png") , emit: pvalues_vs_nes_plot
tuple val(meta), path("*ranked_list_corr_2.png") , emit: ranked_list_corr
tuple val(meta), path("*butterfly_plot.png") , emit: butterfly_plot, optional: true
tuple val(meta), path("*[!gene_set_size|gsea_report|ranked_gene_list]*.tsv"), emit: gene_set_tsv, optional: true
tuple val(meta), path("*[!gsea_report|heat_map_corr_plot|index|pos_snapshot|neg_snapshot]*.html"), emit: gene_set_html, optional: true
tuple val(meta), path("*.rpt") , emit: rpt
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tuple val(meta), path("*index.html") , emit: index_html
tuple val(meta), path("*heat_map_corr_plot.html") , emit: heat_map_corr_plot
tuple val(meta), path("*gsea_report_for_${reference}.tsv") , emit: report_tsvs_ref
tuple val(meta), path("*gsea_report_for_${reference}.html") , emit: report_htmls_ref
tuple val(meta), path("*gsea_report_for_${target}.tsv") , emit: report_tsvs_target
tuple val(meta), path("*gsea_report_for_${target}.html") , emit: report_htmls_target
tuple val(meta), path("*ranked_gene_list*.tsv") , emit: ranked_gene_list
tuple val(meta), path("*gene_set_sizes.tsv") , emit: gene_set_sizes
tuple val(meta), path("*global_es_histogram.png") , emit: histogram
tuple val(meta), path("*heat_map_1.png") , emit: heatmap
tuple val(meta), path("*pvalues_vs_nes_plot.png") , emit: pvalues_vs_nes_plot
tuple val(meta), path("*ranked_list_corr_2.png") , emit: ranked_list_corr
tuple val(meta), path("*butterfly_plot.png") , emit: butterfly_plot, optional: true
tuple val(meta), path("*[!gene_set_size|gsea_report|ranked_gene_list]*.tsv") , emit: gene_set_tsv, optional: true
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tuple val(meta), path("*[!gsea_report|heat_map_corr_plot|index|pos_snapshot|neg_snapshot]*.html") , emit: gene_set_html, optional: true
tuple val(meta), path("*[!butterfly|enplot|global_es_histogram|gset_rnd_es_dist|heat_map|pvalues_vs_nes_plot|ranked_list_corr]*.png"), emit: gene_set_heatmap, optional: true
tuple val(meta), path("*_snapshot*.html") , emit: snapshot, optional: true
tuple val(meta), path("*enplot*.png") , emit: gene_set_enplot, optional: true
tuple val(meta), path("*gset_rnd_es_dist*.png") , emit: gene_set_dist, optional: true
tuple val(meta), path("*.zip") , emit: archive, optional: true
path "versions.yml" , emit: versions
tuple val(meta), path("*_snapshot*.html") , emit: snapshot, optional: true
tuple val(meta), path("*enplot*.png") , emit: gene_set_enplot, optional: true
tuple val(meta), path("*gset_rnd_es_dist*.png") , emit: gene_set_dist, optional: true
tuple val(meta), path("*.zip") , emit: archive, optional: true
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when

script:
def VERSION = '4.3.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"

// Remove any trailing dots from prefix when passed as report label, so
// GSEA doesn't produce double-dotted top-level outputs
def rpt_label = prefix.replaceAll('\\.$', '')

def rpt_label = prefix.replaceAll('\\.$', '') // Remove any trailing dots from prefix when passed as report label, so GSEA doesn't produce double-dotted top-level outputs
def chip_command = chip ? "-chip $chip -collapse true" : ''
def VERSION = '4.3.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.

"""
# Run GSEA

Expand Down Expand Up @@ -78,9 +75,34 @@ process GSEA_GSEA {
sed -i.bak "s/\$f/${prefix}\${f}/g" *.rpt *.html && rm *.bak
done

#Version command uses both conda and micromamba so that it works with both wave containers and conda environments
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cat <<-END_VERSIONS > versions.yml
"${task.process}":
gsea: $VERSION
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
def VERSION = '4.3.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
"""
touch ${prefix}.rpt
touch ${prefix}.index.html
touch ${prefix}.heat_map_corr_plot.html
touch ${prefix}.gsea_report_for_${reference}.tsv
touch ${prefix}.gsea_report_for_${reference}.html
touch ${prefix}.gsea_report_for_${target}.tsv
touch ${prefix}.gsea_report_for_${target}.html
touch ${prefix}.ranked_gene_list*.tsv
touch ${prefix}.gene_set_sizes.tsv
touch ${prefix}.global_es_histogram.png
touch ${prefix}.heat_map_1.png
touch ${prefix}.pvalues_vs_nes_plot.png
touch ${prefix}.ranked_list_corr_2.png

#Version command uses both conda and micromamba so that it works with both wave containers and conda environments
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gsea: $VERSION
"""
}
69 changes: 69 additions & 0 deletions modules/nf-core/gsea/gsea/tests/main.nf.test
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@@ -0,0 +1,69 @@
nextflow_process {

name "Test Process GSEA_GSEA"
script "../main.nf"
process "GSEA_GSEA"
tag "modules"
tag "modules_nfcore"
tag "gsea_gsea"
tag "gsea"
tag "gsea/gsea"

test("test") {

when {
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_treatment_Control_Treated.gct", checkIfExists:true), file("https://github.com/nf-core/test-datasets/raw/refs/heads/differentialabundance/modules_testdata/Condition_genotype_WT_KO.cls", checkIfExists:true), 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[1] = ['WT', 'KO']
input[2] = file("https://github.com/nf-core/test-datasets/raw/refs/heads/differentialabundance/modules_testdata/Mus_musculus.anno.feature_metadata.chip", checkIfExists:true)
"""
}
}

then {
assertAll (
{ assert process.success },
{ assert snapshot(
process.out.rpt.collect{ meta,rpt -> file(rpt).name }, //assert unstable file,
process.out.index_html.collect{ meta,index_html -> file(index_html).name }, //assert unstable file
process.out.heat_map_corr_plot,
process.out.report_tsvs_ref.collect{ meta,report_tsvs_ref -> file(report_tsvs_ref).name },
process.out.report_htmls_ref.collect{ meta,report_htmls_ref -> file(report_htmls_ref).name }, //assert unstable file
process.out.report_tsvs_target.collect{ meta,report_tsvs_target -> file(report_tsvs_target).name }, //assert unstable file
process.out.report_htmls_target.collect{ meta,report_htmls_target -> file(report_htmls_target).name }, //assert unstable file
process.out.ranked_gene_list.collect{ meta,ranked_gene_list -> file(ranked_gene_list).name }, //assert unstable file
process.out.gene_set_sizes,
process.out.histogram.collect{ meta,histogram -> file(histogram).name }, //assert unstable file
process.out.heatmap.collect{ meta,heatmap -> file(heatmap).name }, //assert unstable file
process.out.pvalues_vs_nes_plot.collect{ meta,pvalues_vs_nes_plot -> file(pvalues_vs_nes_plot).name }, //assert unstable file
process.out.ranked_list_corr.collect{ meta,ranked_list_corr -> file(ranked_list_corr).name }, //assert unstable file
process.out.versions
).match()
}
)
}
}

test("stub") {

options "-stub"

when {
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_treatment_Control_Treated.gct", checkIfExists:true), file("https://github.com/nf-core/test-datasets/raw/refs/heads/differentialabundance/modules_testdata/Condition_genotype_WT_KO.cls", checkIfExists:true), 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[1] = ['WT', 'KO']
input[2] = file("https://github.com/nf-core/test-datasets/raw/refs/heads/differentialabundance/modules_testdata/Mus_musculus.anno.feature_metadata.chip", checkIfExists:true)
"""
}
}

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