Merge pull request nf-core#459 from genomic-medicine-sweden/nextflow_val

feat added specific values for some samplesheet params
genomic-medicine-sweden · Dec 22, 2023 · 42f9d64 · 42f9d64
2 parents e3160e5 + 5a2c55c
commit 42f9d64
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Showing 4 changed files with 10 additions and 8 deletions.
diff --git 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": {

diff --git 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
@@ -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(' ') }

diff --git 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
         }
     }