add --efo_id parameter

PGScatalog · Jul 31, 2024 · cc11c8a · cc11c8a
1 parent a2dc50a
commit cc11c8a
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Showing 3 changed files with 16 additions and 2 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -14,6 +14,7 @@ params {
     scorefile                  = null
     pgs_id                     = null
     trait_efo                  = null
+    efo_id                     = null // synonym for trait_efo, which is deprecated
     pgp_id                     = null
     efo_direct                 = false
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -55,10 +55,14 @@
           "description": "A comma separated list of PGS Catalog publications, e.g. PGP000001",
           "pattern": "PGP[0-9]{6}"
         },
-        "trait_efo": {
+        "efo_id": {
           "type": "string",
           "description": "A comma separated list of PGS Catalog EFO traits, e.g. EFO_0004214"
         },
+        "trait_efo": {
+          "type": "string",
+          "description": "DEPRECATED: A comma separated list of PGS Catalog EFO traits, e.g. EFO_0004214"
+        },
         "efo_direct": {
           "type": "boolean",
           "description": "Return only PGS tagged with exact EFO term (e.g. no PGS for child/descendant terms in the ontology)"

diff --git a/workflows/pgsc_calc.nf b/workflows/pgsc_calc.nf
@@ -170,7 +170,16 @@ workflow PGSCCALC {
     // make sure accessions look sensible before querying PGS Catalog
     def pgs_id = WorkflowPgscCalc.prepareAccessions(params.pgs_id, "pgs_id")
     def pgp_id = WorkflowPgscCalc.prepareAccessions(params.pgp_id, "pgp_id")
-    def trait_efo = WorkflowPgscCalc.prepareAccessions(params.trait_efo, "trait_efo")
+
+    // temporarily handle parameter synonym (--trait_efo -> --efo_id) 
+    def traits = [params.trait_efo, params.efo_id].findAll { it != null }.join(",")
+
+    if (params.trait_efo) {
+        println "WARNING: --trait_efo is deprecated and will be removed in a future release, please use --efo_id"
+    }
+
+    def trait_efo = WorkflowPgscCalc.prepareAccessions(traits, "trait_efo")
+
     def accessions = pgs_id + pgp_id + trait_efo
 
     if (!accessions.every { it.value == "" }) {