add mount of licensed tools

conf/modules.config

@@ -211,30 +211,28 @@ process {
     withName: INTERPROSCAN {
         cpus   = 16
         memory = { 12.GB * task.attempt }
-        ext.args =
-            "--iprlookup " +
-            "--goterms " +
-            "--applications " + [
+        ext.args = {
+            def applications = [
                 "TIGRFAM",
                 "SFLD",
                 "SUPERFAMILY",
-                "Gene3D",
-                "Hamap",
-                "Coils",
+                "GENE3D",
+                "HAMAP",
+                "COILS",
                 "CDD",
                 "PRINTS",
                 "PIRSF",
-                "ProSiteProfiles",
-                "ProSitePatterns",
-                "PfamA",
-                "MobiDBLite",
-                "SMART",
-                //"SignalP_GRAM_POSITIVE",
-                //"SignalP_GRAM_NEGATIVE",
-                //"SignalP_EUK",
-                //"Phobius",
-                //"TMHMM",
-        ].join(",")
+                "PROSITEPROFILES",
+                "PROSITEPATTERNS",
+                "PFAM",
+                "MOBIDBLITE",
+                "SMART"
+            ]
+            if ( params.interpro_licensed_software ) {
+                applications << "SIGNALP"
+            }
+            return "--iprlookup --goterms --pathways --applications " + applications.join(",")
+        }
 
         // We override the prefix of the output here because the input is chunked and joined with CAT_CAT
         // and to avoid naming collisions we use the name of the input (which comes from SEQKIT_SPLIT2) that

conf/test_full.config

@@ -28,7 +28,7 @@ params {
     rfam_cm                            = "${projectDir}/tests/reference_databases/rrnas_rfam/ribo.cm"
     rfam_claninfo                      = "${projectDir}/tests/reference_databases/rrnas_rfam/ribo.clan_info"
 
-    interproscan_database              = "${projectDir}/modules/ebi-metagenomics/interproscan/tests/fixtures/interproscan_db/data"
+    interproscan_database              = "${projectDir}/modules/ebi-metagenomics/interproscan/tests/fixtures/interproscan_db"
     interproscan_database_version      = "5.73-104.0"
 
     eggnog_data_dir                    = "${projectDir}/tests/reference_databases/eggnog_mapper/"

modules/ebi-metagenomics/interproscan/main.nf

@@ -5,11 +5,19 @@ process INTERPROSCAN {
     container 'microbiome-informatics/interproscan:5.73-104.0'
 
     containerOptions {
-        if (workflow.containerEngine == 'singularity') {
-            return "--bind ${interproscan_db}:/opt/interproscan/data"
-        } else {
-            return "-v ${task.workDir}/${interproscan_db}:/opt/interproscan/data"
+        def containerArgs = []
+        def mountArg = (workflow.containerEngine == 'singularity') ? "--bind" : "--volume"
+
+        containerArgs << "${mountArg} ${task.workDir}/${interproscan_db}/data:/opt/interproscan/data"
+
+        if ( params.interpro_licensed_software ) {
+            def licensedSoftwarePath = "${task.workDir}/${interproscan_db}/licensed"
+            containerArgs << "${mountArg} ${licensedSoftwarePath}:/opt/interproscan/licensed"
+            // This override is needed otherwise it fails because this path seems to be hardcoded in the container
+            containerArgs << "${mountArg} ${licensedSoftwarePath}/signalp:/usr/opt/www/pub/CBS/services/SignalP-4.1/signalp-4.1"
         }
+
+        return containerArgs.join(' ')
     }
 
     input:

nextflow.config

@@ -32,6 +32,7 @@ params {
     // TODO: cat db version from @Sonya
     interproscan_database              = null
     interproscan_database_version      = "5.73-104.0"
+    interpro_licensed_software         = false
 
     eggnog_database                    = null
     eggnog_diamond_database            = null

nextflow_schema.json

@@ -129,6 +129,12 @@
                     "description": "The version of the interproscan database.",
                     "fa_icon": "fas fa-code-branch"
                 },
+                "interpro_licensed_software": {
+                    "type": "boolean",
+                    "default": false,
+                    "description": "Enables the use of licensed software in InterProScan. Set to true if the required licensed software is in the licensed database folder, https://interproscan-docs.readthedocs.io/en/v5/HowToRun.html#included-analyses.",
+                    "fa_icon": "fas fa-file-contract"
+                },
                 "eggnog_database": {
                     "type": "string",
                     "format": "file-path",