add option to provide custom amrfinder or mlst databases

bactopia · May 1, 2024 · 16545ce · 16545ce
1 parent 27290bd
commit 16545ce
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Showing 6 changed files with 20 additions and 3 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -22,6 +22,7 @@ description: A full list of Bactopia releases and a description of the changes.
     - now required non-integer values for `--max_time` (e.g. `4.h`) and `--max_memory` (e.g. `8.GB`)
     - always import `base.config`
 - `amrfinderplus` by combining results from genes, proteins and gff (coordinates)
+- `--amrfinder_db` and `--mlst_db` to specify custom databases
 
 ### `Fixed`
 

diff --git a/modules/nf-core/amrfinderplus/run/params.config b/modules/nf-core/amrfinderplus/run/params.config
@@ -12,4 +12,5 @@ params {
     report_common = false
     report_all_equal = false
     amrfinder_opts = ""
+    amrfinder_db = ""
 }
diff --git a/modules/nf-core/amrfinderplus/run/params.json b/modules/nf-core/amrfinderplus/run/params.json
@@ -62,6 +62,12 @@
                     "type": "string",
                     "description": "Extra AMRFinder+ options in quotes.",
                     "fa_icon": "fas fa-expand-arrows-alt"
+                },
+                "amrfinder_db": {
+                    "type": "string",
+                    "default": "",
+                    "description": "A custom AMRFinder+ database to use. Contents should be within a directory called 'amrfinderplus'",
+                    "fa_icon": "fas fa-expand-arrows-alt"
                 }
             }
         }

diff --git a/modules/nf-core/mlst/params.json b/modules/nf-core/mlst/params.json
@@ -33,7 +33,7 @@
                 "minscore": {
                     "type": "integer",
                     "default": 50,
-                    "description": "Minumum score out of 100 to match a scheme",
+                    "description": "Minimum score out of 100 to match a scheme",
                     "fa_icon": "fas fa-expand-arrows-alt"
                 },
                 "nopath": {

diff --git a/subworkflows/local/amrfinderplus/main.nf b/subworkflows/local/amrfinderplus/main.nf
@@ -28,7 +28,11 @@ workflow AMRFINDERPLUS {
     ch_merged_reports = Channel.empty()
 
     // Run AMRFinder
-    AMRFINDERPLUS_RUN ( fasta, db )
+    if (params.amrfinder_db) {
+        AMRFINDERPLUS_RUN(fasta, file(params.amrfinder_db))
+    } else {
+        AMRFINDERPLUS_RUN(fasta, db)
+    }
     ch_versions = ch_versions.mix(AMRFINDERPLUS_RUN.out.versions.first())
 
     // Merge results

diff --git a/subworkflows/local/mlst/main.nf b/subworkflows/local/mlst/main.nf
@@ -22,7 +22,12 @@ workflow MLST {
     main:
     ch_versions = Channel.empty()
 
-    MLST_MODULE(fasta, db)
+    if (params.mlst_db) {
+        MLST_MODULE(fasta, file(params.mlst_db))
+    } else {
+        MLST_MODULE(fasta, db)
+    }
+
     ch_versions = ch_versions.mix(MLST_MODULE.out.versions.first())
 
     // Merge results