uncomment dada_get_unmerged, fix typo in params-ngs16s

nhoffman · May 18, 2022 · 018dae0 · 018dae0
1 parent 92f9c2f
commit 018dae0
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Showing 2 changed files with 15 additions and 15 deletions.
diff --git a/main.nf b/main.nf
@@ -297,25 +297,25 @@ process dada_dereplicate {
     """
 }
 
-// process dada_get_unmerged {
+process dada_get_unmerged {
 
-//     label 'med_cpu_mem'
+    label 'med_cpu_mem'
 
-//     input:
-//         val sampleid from dada_dereplicate_samples
-//         file("dada_params.json") from maybe_local(params.dada_params)
-//         file dada_rds from dada_data
+    input:
+        val sampleid from dada_dereplicate_samples
+        file("dada_params.json") from maybe_local(params.dada_params)
+        file dada_rds from dada_data
 
-//     output:
-//         file("unmerged_*.fasta") into dada_unmerged
+    output:
+        file("unmerged_*.fasta") into dada_unmerged
 
-//     publishDir "${params.output}/dada/${sampleid}/", overwrite: true, mode: 'copy'
+    publishDir "${params.output}/dada/${sampleid}/", overwrite: true, mode: 'copy'
 
-//     """
-//     get_unmerged.R ${dada_rds} \
-//         --forward-seqs unmerged_F.fasta --reverse-seqs unmerged_R.fasta
-//     """
-// }
+    """
+    get_unmerged.R ${dada_rds} \
+        --forward-seqs unmerged_F.fasta --reverse-seqs unmerged_R.fasta
+    """
+}
 
 
 process combined_overlaps {

diff --git a/params-ngs16s.json b/params-ngs16s.json
@@ -3,7 +3,7 @@
   "fastq_list": "test-single/fastq-list.txt",
   "output": "output-single",
   "index_file_type": "single",
-  "dada_params": "data/dada_params_ngs16s.json"
+  "dada_params": "data/dada_params_ngs16s.json",
   "bidirectional": false,
   "alignment_model": "data/ssu-align-0.1.1-bacteria-0p1.cm"
 }