fix initialization

qbic-pipelines · Nov 19, 2024 · b56df87 · b56df87
1 parent 132e190
commit b56df87
Showing 1 changed file with 14 additions and 19 deletions.
diff --git a/subworkflows/local/utils_nfcore_vcftomaf_pipeline/main.nf b/subworkflows/local/utils_nfcore_vcftomaf_pipeline/main.nf
@@ -71,27 +71,22 @@ workflow PIPELINE_INITIALISATION {
     //
     // Create channel from input file provided through params.input
     //
-
-    Channel
+    ch_samplesheet = Channel
         .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
-        .map {
-            meta, fastq_1, fastq_2 ->
-                if (!fastq_2) {
-                    return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ]
-                } else {
-                    return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ]
-                }
-        }
-        .groupTuple()
-        .map { samplesheet ->
-            validateInputSamplesheet(samplesheet)
+        .map{ meta, normal_id, tumor_id, vcf_normal_id, vcf_tumor_id, vcf, index ->
+
+            meta.index               = index     ? true      : false
+
+            if (normal_id) {
+                meta.normal_id       = normal_id
+                meta.vcf_normal_id   = vcf_normal_id
+            }
+            if (tumor_id) {
+                meta.tumor_id        = tumor_id
+                meta.vcf_tumor_id    = vcf_tumor_id
+            }
+            return [meta, vcf, index] // it[0], it[1], it[2]
         }
-        .map {
-            meta, fastqs ->
-                return [ meta, fastqs.flatten() ]
-        }
-        .set { ch_samplesheet }
-
     emit:
     samplesheet = ch_samplesheet
     versions    = ch_versions