remove lib

Clinical-Genomics · Jan 15, 2025 · 4e71e74 · 4e71e74
1 parent 7a81697
commit 4e71e74
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Showing 4 changed files with 60 additions and 53 deletions.
diff --git a/lib/CustomFunctions.groovy b/lib/CustomFunctions.groovy
diff --git a/main.nf b/main.nf
@@ -34,14 +34,18 @@ workflow NFCORE_RAREDISEASE {
 
     take:
     samplesheet // channel: samplesheet read in from --input
+    samples
+    case_info
 
     main:
 
     //
     // WORKFLOW: Run pipeline
     //
     RAREDISEASE (
-        samplesheet
+        samplesheet,
+        samples,
+        case_info
     )
     emit:
     multiqc_report = RAREDISEASE.out.multiqc_report // channel: /path/to/multiqc_report.html
@@ -71,7 +75,9 @@ workflow {
     // WORKFLOW: Run main workflow
     //
     NFCORE_RAREDISEASE (
-        PIPELINE_INITIALISATION.out.samplesheet
+        PIPELINE_INITIALISATION.out.samplesheet,
+        PIPELINE_INITIALISATION.out.samples,
+        PIPELINE_INITIALISATION.out.case_info
     )
     //
     // SUBWORKFLOW: Run completion tasks

diff --git a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf
@@ -102,8 +102,19 @@ workflow PIPELINE_INITIALISATION {
         }
         .set { ch_samplesheet }
 
+    ch_samples   = ch_samplesheet.map { meta, fastqs ->
+                        new_id = meta.sample
+                        new_meta = meta - meta.subMap('lane', 'read_group') + [id:new_id]
+                        return new_meta
+                    }.unique()
+
+    ch_case_info = ch_samples.toList().map { createCaseChannel(it) }
+
+
     emit:
     samplesheet = ch_samplesheet
+    samples     = ch_samples
+    case_info   = ch_case_info
     versions    = ch_versions
 }
 
@@ -160,6 +171,44 @@ workflow PIPELINE_COMPLETION {
     FUNCTIONS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
+
+def boolean isNonZeroNonEmpty(value) {
+        return (value instanceof String && value != "" && value != "0") ||
+                (value instanceof Number && value != 0)
+    }
+
+    // Function to get a list of metadata (e.g. case id) for the case [ meta ]
+def createCaseChannel(List rows) {
+    def case_info    = [:]
+    def probands     = [] as Set
+    def upd_children = [] as Set
+    def father       = ""
+    def mother       = ""
+
+    rows.each { item ->
+        if (item?.phenotype == 2) {
+            probands << item.sample
+        }
+        if (isNonZeroNonEmpty(item?.paternal) && isNonZeroNonEmpty(item?.maternal)) {
+            upd_children << item.sample
+        }
+        if (isNonZeroNonEmpty(item?.paternal)) {
+            father = item.paternal
+        }
+        if (isNonZeroNonEmpty(item?.maternal)) {
+            mother = item.maternal
+        }
+    }
+
+    case_info.father       = father
+    case_info.mother       = mother
+    case_info.probands     = probands.toList()
+    case_info.upd_children = upd_children.toList()
+    case_info.id           = rows[0].case_id
+
+    return case_info
+}
+
 //
 // Check and validate pipeline parameters
 //

diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf
@@ -175,19 +175,14 @@ workflow RAREDISEASE {
 
     take:
     ch_samplesheet // channel: samplesheet read in from --input
+    ch_samples
+    ch_case_info
+
     main:
 
     ch_versions = Channel.empty()
     ch_multiqc_files = Channel.empty()
 
-    ch_samples   = ch_samplesheet.map { meta, fastqs ->
-                        new_id = meta.sample
-                        new_meta = meta - meta.subMap('lane', 'read_group') + [id:new_id]
-                        return new_meta
-                    }.unique()
-
-    ch_case_info = ch_samples.toList().map { CustomFunctions.createCaseChannel(it) }
-
     //
     // Initialize file channels for PREPARE_REFERENCES subworkflow
     //