From f5594e639331e75c320dab6db086d1a1228a4281 Mon Sep 17 00:00:00 2001
From: lucpen <lucia.penaperez@hasta-login.local>
Date: Wed, 20 Dec 2023 13:27:51 +0100
Subject: [PATCH 1/3] feat added specific values for some samplesheet params

---
 assets/schema_input.json | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/assets/schema_input.json b/assets/schema_input.json
index 191f1394..cb881db8 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -39,15 +39,17 @@
                 ]
             },
             "sex": {
-                "type": "string",
+                "type": "integer",
                 "meta": ["sex"],
                 "pattern": "^\\S+$",
+                "enum": [0, 1, 2],
                 "errorMessage": "Sex must be provided and cannot contain spaces"
             },
             "phenotype": {
-                "type": "string",
+                "type": "integer",
                 "meta": ["phenotype"],
                 "pattern": "^\\S+$",
+                "enum": [0, 1, 2],
                 "errorMessage": "Phenotype must be provided and cannot contain spaces"
             },
             "paternal_id": {

From 82a96cb6484234f25c986e56c8d8ee1fdda107fa Mon Sep 17 00:00:00 2001
From: lucpen <lucia.penaperez@hasta-login.local>
Date: Thu, 21 Dec 2023 11:21:33 +0100
Subject: [PATCH 2/3] fix integer to number

---
 workflows/raredisease.nf | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf
index c1b12cd4..c4183c93 100644
--- a/workflows/raredisease.nf
+++ b/workflows/raredisease.nf
@@ -686,16 +686,16 @@ def create_case_channel(List rows) {
     def mother       = ""
 
     for (item in rows) {
-        if (item.phenotype == "2") {
+        if (item.phenotype == 2) {
             probands.add(item.sample)
         }
-        if ( (item.paternal!="0") && (item.paternal!="") && (item.maternal!="0") && (item.maternal!="") ) {
+        if ( (item.paternal!=0) && (item.paternal!="") && (item.maternal!=0) && (item.maternal!="") ) {
             upd_children.add(item.sample)
         }
-        if ( (item.paternal!="0") && (item.paternal!="") ) {
+        if ( (item.paternal!=0) && (item.paternal!="") ) {
             father = item.paternal
         }
-        if ( (item.maternal!="0") && (item.maternal!="") ) {
+        if ( (item.maternal!=0) && (item.maternal!="") ) {
             mother = item.maternal
         }
     }

From 5a2c55c5aae2b0fd89e33737be13b09ab719259e Mon Sep 17 00:00:00 2001
From: lucpen <lucia.penaperez@hasta-login.local>
Date: Fri, 22 Dec 2023 07:18:49 +0100
Subject: [PATCH 3/3] fix

---
 conf/modules/call_repeat_expansions.config  | 2 +-
 conf/modules/generate_cytosure_files.config | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/conf/modules/call_repeat_expansions.config b/conf/modules/call_repeat_expansions.config
index 0509d1e2..13a7e519 100644
--- a/conf/modules/call_repeat_expansions.config
+++ b/conf/modules/call_repeat_expansions.config
@@ -24,7 +24,7 @@ process {
     }
 
     withName: '.*CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER' {
-        ext.args =  { ("${meta.sex}" == '1') ? '--sex male' : '--sex female' }
+        ext.args =  { ("${meta.sex}" == 1) ? '--sex male' : '--sex female' }
         ext.prefix = { "${meta.id}_exphunter" }
     }
 
diff --git a/conf/modules/generate_cytosure_files.config b/conf/modules/generate_cytosure_files.config
index a1600d97..323b64e3 100644
--- a/conf/modules/generate_cytosure_files.config
+++ b/conf/modules/generate_cytosure_files.config
@@ -35,7 +35,7 @@ process {
 
         withName: '.*GENERATE_CYTOSURE_FILES:VCF2CYTOSURE' {
             ext.args = { [
-                meta.sex.equals('1') ? '--sex male' : '--sex female',
+                meta.sex.equals(1) ? '--sex male' : '--sex female',
                 '--size 5000',
                 '--maxbnd 5000'
                 ].join(' ') }