Use singular form for recalibration_table

uclahs-cds · Dec 20, 2023 · a772dae · a772dae
1 parent b83b022
commit a772dae
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Showing 10 changed files with 11 additions and 11 deletions.
diff --git a/README.md b/README.md
@@ -121,7 +121,7 @@ input:
     tumor:
       - "/absolute/path/to/BAM"
       - "/absolute/path/to/BAM"
-  recalibration_tables:
+  recalibration_table:
     - "/absolute/path/to/recalibration/table1"
     - "/absolute/path/to/recalibration/table2"
 ```

diff --git a/config/custom_schema_types.config b/config/custom_schema_types.config
@@ -4,7 +4,7 @@
 custom_schema_types {
     allowed_input_types = [
         'BAM',
-        'recalibration_tables'
+        'recalibration_table'
     ]
     allowed_bam_types = [
         'normal',

diff --git a/config/methods.config b/config/methods.config
@@ -142,10 +142,10 @@ methods {
     }
 
     set_recal_tables = {
-        params.use_recal_tables = params.input.containsKey('recalibration_tables')
+        params.use_recal_tables = params.input.containsKey('recalibration_table')
 
         if (!params.use_recal_tables) {
-            params.input['recalibration_tables'] = ["${params.work_dir}/NO_FILE.grp"]
+            params.input['recalibration_table'] = ["${params.work_dir}/NO_FILE.grp"]
         }
     }
 

diff --git a/config/schema.yaml b/config/schema.yaml
@@ -126,7 +126,7 @@ input:
           type: 'BAMEntryList'
           required: false
           help: 'Input tumor BAMs'
-    recalibration_tables:
+    recalibration_table:
       type: 'RecalibrationTableList'
       required: false
       allow_empty: false

diff --git a/input/recalibrate-BAM-multiple-input-with-recal-table.yaml b/input/recalibrate-BAM-multiple-input-with-recal-table.yaml
@@ -8,7 +8,7 @@ input:
     tumor:
       - "/abosolute/path/to/BAM"
       - "/absolute/path/to/BAM"
-  recalibration_tables:
+  recalibration_table:
     - "/absolute/path/to/recalibration/table/sample1"
     - "/absolute/path/to/recalibration/table/sample2"
     - "/absolute/path/to/recalibration/table/sample3"

diff --git a/input/recalibrate-BAM-normal-only-input-with-recal-table.yaml b/input/recalibrate-BAM-normal-only-input-with-recal-table.yaml
@@ -4,5 +4,5 @@ input:
   BAM:
     normal:
       - "/absolute/path/to/BAM"
-  recalibration_tables:
+  recalibration_table:
     - "/absolute/path/to/recalibration/table"
diff --git a/input/recalibrate-BAM-paired-input-with-recal-table.yaml b/input/recalibrate-BAM-paired-input-with-recal-table.yaml
@@ -6,6 +6,6 @@ input:
       - "/absolute/path/to/BAM"
     tumor:
       - "/absolute/path/to/BAM"
-  recalibration_tables:
+  recalibration_table:
     - "/absolute/path/to/recalibration/table/sample1"
     - "/absolute/path/to/recalibration/table/sample2"
diff --git a/input/recalibrate-BAM-tumor-only-input-with-recal-table.yaml b/input/recalibrate-BAM-tumor-only-input-with-recal-table.yaml
@@ -4,5 +4,5 @@ input:
   BAM:
     tumor:
       - "/absolute/path/to/BAM"
-  recalibration_tables:
+  recalibration_table:
     - "/absolute/path/to/recalibration/table"
diff --git a/main.nf b/main.nf
@@ -23,7 +23,7 @@ Current Configuration:
         bundle_v0_dbsnp138_vcf_gz: ${params.bundle_v0_dbsnp138_vcf_gz}
         bundle_contest_hapmap_3p3_vcf_gz: ${params.bundle_contest_hapmap_3p3_vcf_gz}
         intervals: ${(params.is_targeted) ?: 'WGS'}
-        recalibration_tables: ${params.input.recalibration_tables}
+        Recalibration tables: ${params.input.recalibration_table}
 
     - output: 
         output: ${params.output_dir}

diff --git a/module/base-recalibration.nf b/module/base-recalibration.nf
@@ -199,7 +199,7 @@ workflow recalibrate_base {
         params.bundle_v0_dbsnp138_vcf_gz,
         "${params.bundle_v0_dbsnp138_vcf_gz}.tbi",
         base_recalibrator_intervals,
-        params.input.recalibration_tables,
+        params.input.recalibration_table,
         input_ch_base_recalibrator
     )