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fix(gprofiler2_gost): define the database archive for reproducibility #7450

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fix(gprofiler2_gost): define the database archive for reproducibility #7450

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5d88a0d
fix(gprofiler2_gost): define the database archive for reproducibility
suzannejin Feb 7, 2025
d9fa8e8
fix(gprofiler2_gost): also update the archive config for the function…
suzannejin Feb 7, 2025
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7 changes: 5 additions & 2 deletions 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 @@ -139,7 +139,8 @@ opt <- list(
domain_scope = 'annotated',
min_diff = 1,
round_digits = -1,
palette_name = 'Blues'
palette_name = 'Blues',
archive = 'gprofiler'
)

opt_types <- lapply(opt, class)
Expand Down Expand Up @@ -235,7 +236,9 @@ if (nrow(de.genes) > 0) {
} else if (!is.null(opt\$organism)) {

# Next, check if organism was provided. Get the GMT file from gprofiler and save both the full file as well as the filtered one to metadata
gmt_url <- paste0("https://biit.cs.ut.ee/gprofiler//static/gprofiler_full_", opt\$organism, ".ENSG.gmt")
base_url <- paste0("https://biit.cs.ut.ee/", opt\$archive)
gmt_url <- paste0(base_url, "//static/gprofiler_full_", opt\$organism, ".ENSG.gmt")
set_base_url(base_url)
tryCatch(
{
gmt_path <- paste0("gprofiler_full_", opt\$organism, ".ENSG.gmt")
Expand Down
3 changes: 2 additions & 1 deletion modules/nf-core/gprofiler2/gost/tests/main.nf.test
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Expand Up @@ -46,7 +46,8 @@ nextflow_process {
((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}\"")
((params.gprofiler2_sources == null) ? '' : "--sources \"${params.gprofiler2_sources}\""),
"--archive gprofiler_archive3/e111_eg58_p18"
].join(' ').trim()
}
process {
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/gprofiler2/gost/tests/nextflow.config
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@@ -1,3 +1,3 @@
process {
ext.args = params.module_args
}
}
3 changes: 2 additions & 1 deletion subworkflows/nf-core/differential_functional_enrichment/tests/all.config
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Expand Up @@ -45,7 +45,8 @@ process {
"--round_digits 4",
"--palette_name Blues",
"--de_id_column gene_id",
"--organism mmusculus"
"--organism mmusculus",
"--archive gprofiler_archive3/e111_eg58_p18"
].join(' ').trim()
}

Expand Down
3 changes: 2 additions & 1 deletion subworkflows/nf-core/differential_functional_enrichment/tests/deseq2_gprofiler2.config
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Expand Up @@ -24,7 +24,8 @@ process {
"--round_digits 4",
"--palette_name Blues",
"--de_id_column gene_id",
"--organism mmusculus"
"--organism mmusculus",
"--archive gprofiler_archive3/e111_eg58_p18"
].join(' ').trim()
}
}
3 changes: 2 additions & 1 deletion subworkflows/nf-core/differential_functional_enrichment/tests/gprofiler2.config
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,8 @@ process {
"--round_digits 4",
"--palette_name Blues",
"--de_id_column gene_id",
"--organism mmusculus"
"--organism mmusculus",
"--archive gprofiler_archive3/e111_eg58_p18"
].join(' ').trim()
}
}
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