Add: Config for deblur workflow

micone/pipelines/modules/denoise_cluster/denoise_cluster/deblur.nf

@@ -1,11 +1,15 @@
 // Step1: Denoise using deblur
 process deblur {
     label 'qiime2'
-    tag "${id}"
+    tag "${meta.id}"
     input:
-        tuple val(id), file(sequence_files), file(manifest_file)
+        tuple val(meta), file(sequence_files), file(manifest_file)
     output:
-        tuple val(id), file('*_otu_table.biom'), file('*_rep_seqs.fasta')
+        tuple val(meta), file('*_otu_table.biom'), file('*_rep_seqs.fasta')
     script:
+        meta.denoise_cluster = "deblur"
+        ncpus = params.denoise_cluster.denoise_cluster['deblur']['ncpus']
+        min_reads = params.denoise_cluster.denoise_cluster['deblur']['min_reads']
+        min_size = params.denoise_cluster.denoise_cluster['deblur']['min_size']
         template 'denoise_cluster/denoise_cluster/deblur.sh'
 }

micone/pipelines/modules/denoise_cluster/denoise_cluster/deblur_workflow.nf

@@ -11,6 +11,7 @@ workflow deblur_workflow {
             | deblur \
             | hashing3
     emit:
-        // has `publishDir` -> ${params.output_dir}/${task.process}/${id}
+        // hashing3 has publishDir
+        // tuple val(meta), file('otu_table.biom'), file('rep_seqs.fasta')
         hashing3.out
 }

micone/pipelines/templates/denoise_cluster/denoise_cluster/deblur.sh

@@ -11,15 +11,15 @@ deblur workflow \
     --output-dir deblur_output \
     -t -1 \
     --left-trim-length 0 \
-    --min-reads ${params.deblur.min_reads} \
-    --min-size ${params.deblur.min_size} \
-    --jobs-to-start ${params.deblur.ncpus} \
+    --min-reads ${min_reads} \
+    --min-size ${min_size} \
+    --jobs-to-start ${ncpus} \
     --keep-tmp-files
 
 # Build otu table and rep seqs for the step before chimera checking
 mkdir otu_table
 deblur build-biom-table \
-    --min-reads ${params.deblur.min_reads} \
+    --min-reads ${min_reads} \
     --file_type .trim.derep.no_artifacts.msa.deblur \
     deblur_output/deblur_working_dir \
     otu_table