Add: updateMeta to other misc. modules

1. demultiplexing_illumina 2. biom2tsv
segrelab · Sep 29, 2021 · d53f2f6 · d53f2f6
1 parent cee11ec
commit d53f2f6
Show file tree

Hide file tree

Showing 2 changed files with 12 additions and 8 deletions.
diff --git a/micone/pipelines/modules/denoise_cluster/sequence_processing/demultiplexing_illumina.nf b/micone/pipelines/modules/denoise_cluster/sequence_processing/demultiplexing_illumina.nf
@@ -1,13 +1,16 @@
+include { updateMeta } from '../../../functions/functions.nf'
+
 // demultiplex
 process demultiplexing_illumina {
     label 'qiime2'
-    tag "${meta.id}"
+    tag "${new_meta.id}"
     input:
         tuple val(meta), file(sequence_artifact), file(mapping_file)
     output:
-        tuple val(meta), file('*_demux.qza')
+        tuple val(new_meta), file('*_demux.qza')
     script:
-        meta.demultiplexing = "illumina"
+        new_meta = updateMeta(meta)
+        new_meta.demultiplexing = 'illumina'
         rev_comp_barcodes = params.denoise_cluster.sequence_processing['demultiplexing_illumina']['rev_comp_barcodes']
         rev_comp_mapping_barcodes = params.denoise_cluster.sequence_processing['demultiplexing_illumina']['rev_comp_mapping_barcodes']
         rcb = rev_comp_barcodes == 'True' ? '--p-rev-comp-barcodes' : '--p-no-rev-comp-barcodes'

diff --git a/micone/pipelines/modules/otu_processing/export/biom2tsv.nf b/micone/pipelines/modules/otu_processing/export/biom2tsv.nf
@@ -1,17 +1,18 @@
-include { getHierarchy } from '../../../functions/functions.nf'
+include { getHierarchy; updateMeta } from '../../../functions/functions.nf'
 
 process biom2tsv {
     label 'micone'
-    tag "${meta.id}"
-    publishDir "${params.output_dir}/${f[0]}/export/${f[1]}/${meta.id}",
+    tag "${new_meta.id}"
+    publishDir "${params.output_dir}/${f[0]}/export/${f[1]}/${new_meta.id}",
         mode: 'copy',
         overwrite: true
     input:
         tuple val(meta), val(tax_level), file(otu_file), file(children_file)
     output:
-        tuple val(meta), file("*_otu.tsv"), file("*_obs_metadata.csv"), file("*_sample_metadata.tsv"), file(children_file)
+        tuple val(new_meta), file("*_otu.tsv"), file("*_obs_metadata.csv"), file("*_sample_metadata.tsv"), file(children_file)
     script:
-        meta.tax_level = tax_level
+        new_meta = updateMeta(meta)
+        new_meta.tax_level = tax_level
         String task_process = "${task.process}"
         f = getHierarchy(task_process)
         template 'otu_processing/export/biom2tsv.py'