Add: naive_bayes workflow

micone/pipelines/modules/tax_assignment/assign/naive_bayes_workflow.nf

@@ -0,0 +1,26 @@
+include { naive_bayes } from './naive_bayes.nf'
+include { add_md2biom } from './add_md2biom.nf'
+
+// NOTE: We try to simplify the workflow by requiring the user to pre-train the classifier
+
+workflow blast_workflow {
+    take:
+        // tuple val(id), file(rep_seqs)
+        rep_seqs_channel
+        // tuple val(id), file(sample_metadata)
+        otu_table_channel
+        // tuple val(id), file(sample_metadata)
+        sample_metadata_channel
+        // TODO: rep_seqs, otu_table and sample_metadata should ideally be in one channel
+        // otu_table and rep_seqs come out of the same channel but sample_metadata is input
+    main:
+        // TODO: The classifier object should be passed in as `${params.naive_bayes.classifier}`
+        rep_seqs_channel \
+            | naive_bayes \
+            | join(otu_table_channel) \
+            | join(sample_metadata_channel) \
+            | add_md2biom
+    emit:
+        // has `publishDir` -> ${params.output_dir}/${task.process}/${id}
+        add_md2biom.out
+}