Add: Data ingestion workflow for network_inference_workflow

micone/pipelines/modules/utils/ni_data_ingestion.nf

@@ -0,0 +1,39 @@
+// input:
+// samplesheet
+// id,otu_table,obs_metadata,sample_metadata,children_map
+// output1:
+// tuple val(meta), file(otu_table), file(obs_metadata), file(sample_metadata), file(children_map)
+
+workflow ni_data_ingestion {
+    take:
+    samplesheet
+
+    main:
+    samplesheet
+        .splitCsv(header: true, sep:',')
+        .map { create_ni_channels(it) }
+        .set { result }
+
+    emit:
+    result
+}
+
+def create_ni_channels(LinkedHashMap row) {
+    def meta = [:]
+    meta.id = row.id
+    def array = []
+    if (!file(row.otu_table).exists()) {
+        exit 1, "ERROR: Please check input samplesheet -> Otu_Table file does not exist!\n${row.sequences}"
+    }
+    if (!file(row.obs_metadata).exists()) {
+        exit 1, "ERROR: Please check input samplesheet -> Obs_Metadata file does not exist!\n${row.barcodes}"
+    }
+    if (!file(row.sample_metadata).exists()) {
+        exit 1, "ERROR: Please check input samplesheet -> Sample_Metadata file does not exist!\n${row.sample_metadata}"
+    }
+    if (!file(row.children_map).exists()) {
+        exit 1, "ERROR: Please check input samplesheet -> Children_Map file does not exist!\n${row.children_map}"
+    }
+    array = [ meta, file(row.otu_table), file(row.obs_metadata), file(row.sample_metadata), file(row.children_map) ]
+    return array
+}