Fix: DC workflow ingestion script

micone/pipelines/modules/utils/dc_data_ingestion.nf

@@ -1,12 +1,11 @@
 // input:
 // samplesheet
-// id,sequences,barcodes,mapping,sample_metadata
+// id,trimmed_sequences,manifest,sample_metadata
 // output1:
-// tuple val(meta), file(sequence_files), file(barcode_files), file(mapping_files)
+// tuple val(meta), file(trimmed_sequences), file(manifest_file)
 // output2:
 // tuple val(meta), file(sample_metadata_files)
 
-// TODO: FIXME: Update this
 workflow dc_data_ingestion {
     take:
     samplesheet
@@ -16,8 +15,8 @@ workflow dc_data_ingestion {
         .splitCsv(header: true, sep: ',')
         .map { create_dc_channels(it) }
         .multiMap { it ->
-            reads: tuple(it[0], it[1], it[2], it[3])
-            sample_md: tuple(it[0], it[4])
+            reads: tuple(it[0], it[1], it[2])
+            sample_md: tuple(it[0], it[3])
         }
         .set { result }
 
@@ -31,18 +30,15 @@ def create_dc_channels(LinkedHashMap row) {
     def meta = [:]
     meta.id = row.id
     def array = []
-    if (!file(row.sequences).exists()) {
-        exit 1, "ERROR: Please check input samplesheet -> Sequences file does not exist!\n${row.sequences}"
+    if (!file(row.trimmed_sequences).exists()) {
+        exit 1, "ERROR: Please check input samplesheet -> Trimmed_Sequences file does not exist!\n${row.trimmed_sequences}"
     }
-    if (!file(row.barcodes).exists()) {
-        exit 1, "ERROR: Please check input samplesheet -> Barcodes file does not exist!\n${row.barcodes}"
-    }
-    if (!file(row.mapping).exists()) {
-        exit 1, "ERROR: Please check input samplesheet -> Mapping file does not exist!\n${row.mapping}"
+    if (!file(row.manifest).exists()) {
+        exit 1, "ERROR: Please check input samplesheet -> Manifest file does not exist!\n${row.manifest}"
     }
     if (!file(row.sample_metadata).exists()) {
         exit 1, "ERROR: Please check input samplesheet -> Sample_Metadata file does not exist!\n${row.sample_metadata}"
     }
-    array = [ meta, file(row.sequences), file(row.barcodes), file(row.mapping), file(row.sample_metadata) ]
+    array = [ meta, file(row.trimmed_sequences), file(row.manifest), file(row.sample_metadata) ]
     return array
 }