fix(gprofiler2_gost): define the database archive for reproducibility

nf-core · Feb 7, 2025 · 5d88a0d · 5d88a0d
1 parent c18de39
commit 5d88a0d
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Showing 3 changed files with 8 additions and 4 deletions.
diff --git a/modules/nf-core/gprofiler2/gost/templates/gprofiler2_gost.R b/modules/nf-core/gprofiler2/gost/templates/gprofiler2_gost.R
@@ -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)
@@ -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")

diff --git a/modules/nf-core/gprofiler2/gost/tests/main.nf.test b/modules/nf-core/gprofiler2/gost/tests/main.nf.test
@@ -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 {

diff --git a/modules/nf-core/gprofiler2/gost/tests/nextflow.config b/modules/nf-core/gprofiler2/gost/tests/nextflow.config
@@ -1,3 +1,3 @@
 process {
     ext.args = params.module_args
-}
+}