Included @scwatts's suggestions for using existing functions to extra…

…ct cancer_type information from info column in samplesheet
nf-core · Jan 28, 2025 · 15288f9 · 15288f9
1 parent b505f6b
commit 15288f9
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Showing 3 changed files with 8 additions and 15 deletions.
diff --git a/lib/Utils.groovy b/lib/Utils.groovy
@@ -92,11 +92,12 @@ class Utils {
                                 info_data[info_field_enum] = v
                             }
 
-                    }
+                        // Added cancer type to metamap    
+                        if (info_data.containsKey(Constants.InfoField.CANCER_TYPE)) {
+                            meta[Constants.InfoField.CANCER_TYPE] = info_data[Constants.InfoField.CANCER_TYPE]
+                            log.info "Added cancer type to meta: ${meta[Constants.InfoField.CANCER_TYPE]}"
+                        }
 
-                    // Process
-                    if (info_data.containsKey(Constants.InfoField.CANCER_TYPE)) {
-                        meta[Constants.InfoField.CANCER_TYPE] = info_data[Constants.InfoField.CANCER_TYPE]
                     }
 
                     // Handle inputs appropriately
@@ -405,12 +406,6 @@ class Utils {
         return meta.getOrDefault([Constants.SampleType.NORMAL, Constants.SequenceType.DNA], [:])
     }
 
-    // New method to return the doid of the cancer_type provided by user
-    static public getCancerType(meta) {
-        return meta.getOrDefault(Constants.InfoField.CANCER_TYPE, null)
-    }
-
-
     // Sample names
     static public getTumorDnaSampleName(meta) {
         return getTumorDnaSample(meta)['sample_id']

diff --git a/modules/local/orange/main.nf b/modules/local/orange/main.nf
@@ -51,10 +51,7 @@ process ORANGE {
     def isofox_gene_distribution_arg = isofox_gene_distribution ? "-isofox_gene_distribution ${isofox_gene_distribution}" : ''
     def isofox_alt_sj_arg = isofox_alt_sj ? "-isofox_alt_sj_cohort ${isofox_alt_sj}" : ''
 
-    // def doid_arg = meta.cancer_type ? "-primary_tumor_doids \"${meta.cancer_type}\"" : "-primary_tumor_doids 162"
-    // log.info "${meta}"
-    def doid_arg = meta.containsKey("cancer_type") ? meta.cancer_type : "162"
-    // log.info "Primary tumor DOID: ${doid_arg}"
+    def doid_arg = meta.cancer_type ?: "162"
 
     """
     echo "${pipeline_version_str}" > pipeline_version.txt

diff --git a/subworkflows/local/orange_reporting/main.nf b/subworkflows/local/orange_reporting/main.nf
@@ -179,7 +179,8 @@ workflow ORANGE_REPORTING {
                 key: meta.group_id,
                 id: meta.group_id,
                 tumor_id: Utils.getTumorDnaSampleName(meta),
-                cancer_type: Utils.getCancerType(meta),
+                // cancer_type: Utils.getCancerType(meta),
+                cancer_type: meta[Constants.InfoField.CANCER_TYPE],
             ]
 
             def inputs_selected = inputs.clone()