Add: dada2 workflow

micone/pipelines/modules/denoise_cluster/denoise_cluster/dada2.nf

@@ -1,11 +1,11 @@
 // Step1: Denoise using dada2
 process dada2 {
+    label 'dada2'
     tag "${id}"
-    publishDir "${output_dir}/${id}", mode: 'copy', overwrite: true
     input:
-    tuple val(id), file(sequence_files), file(manifest_file)
+        tuple val(id), file(sequence_files), file(manifest_file)
     output:
-    tuple val(id), file("seq_table.tsv")
+        tuple val(id), file("seq_table.tsv")
     script:
-    template 'denoise_cluster/denoise_cluster/dada2.R'
+        template 'denoise_cluster/denoise_cluster/dada2.R'
 }

micone/pipelines/modules/denoise_cluster/denoise_cluster/dada2_workflow.nf

@@ -0,0 +1,18 @@
+include { dada2 } from './dada2.nf'
+include { make_biom_repseqs } from './make_biom_repseqs.nf'
+include { hashing3 } from './hashing3.nf'
+
+
+workflow dada2_workflow {
+    take:
+        // tuple val(id), file(sequence_files), file(manifest_file)
+        input_channel
+    main:
+        input_channel \
+            | dada2 \
+            | make_biom_repseqs \
+            | hashing3
+    emit:
+        // has `publishDir` -> ${params.output_dir}/${task.process}/${id}
+        hashing3.out
+}

micone/pipelines/modules/denoise_cluster/denoise_cluster/make_biom_repseqs.nf

@@ -1,11 +1,11 @@
 // Step2: Make representative sequences and biom table
 process make_biom_repseqs {
+    label 'dada2'
     tag "${id}"
-    publishDir "${output_dir}/${id}", mode: 'copy', overwrite: true
     input:
-    tuple val(id), file(seq_table_file)
+        tuple val(id), file(seq_table_file)
     output:
-    tuple val(id), file('*.biom'), file('*.fasta')
+        tuple val(id), file('*.biom'), file('*.fasta')
     script:
-    template 'denoise_cluster/denoise_cluster/make_biom_repseqs.py'
+        template 'denoise_cluster/denoise_cluster/make_biom_repseqs.py'
 }