Add: getHierarchy include statement to all process files

micone/pipelines/modules/denoise_cluster/chimera_checking/export_files.nf

@@ -1,3 +1,5 @@
+include { getHierarchy } from ='../../../functions/functions.nf'
+
 // Step3: Export files
 process export_files {
     label 'qiime2'

micone/pipelines/modules/denoise_cluster/denoise_cluster/hashing2.nf

@@ -1,3 +1,5 @@
+include { getHierarchy } from ='../../../functions/functions.nf'
+
 // Step3: Replace the ids with the hashes of the sequences
 process hashing2 {
     label 'qiime1'

micone/pipelines/modules/denoise_cluster/denoise_cluster/hashing3.nf

@@ -1,3 +1,5 @@
+include { getHierarchy } from ='../../../functions/functions.nf'
+
 // Step3: Replace the ids with hashes of the sequences
 process hashing3 {
     label 'dada2'

micone/pipelines/modules/denoise_cluster/sequence_processing/export_sequences.nf

@@ -1,3 +1,5 @@
+include { getHierarchy } from ='../../../functions/functions.nf'
+
 // Export the sequences and fix the manifest file
 process export_sequences {
     label 'qiime2'

micone/pipelines/modules/denoise_cluster/sequence_processing/join_reads.nf

@@ -1,3 +1,5 @@
+include { getHierarchy } from ='../../../functions/functions.nf'
+
 // Join reads
 process join_reads {
     label 'qiime1'

micone/pipelines/modules/denoise_cluster/sequence_processing/quality_analysis.nf

@@ -1,3 +1,5 @@
+include { getHierarchy } from ='../../../functions/functions.nf'
+
 // Identify positions on the front and the tail that need to be trimmed based on
 // a. quality and b. sequence retainment
 process quality_analysis {

micone/pipelines/modules/denoise_cluster/sequence_processing/trimming.nf

@@ -1,3 +1,5 @@
+include { getHierarchy } from ='../../../functions/functions.nf'
+
 // Trimming the sequences using cutadapt
 process trimming {
     label 'qiime2'

micone/pipelines/modules/network_inference/bootstrap/pvalue.nf

@@ -1,3 +1,5 @@
+include { getHierarchy } from ='../../../functions/functions.nf'
+
 process pvalues {
     label 'sparcc'
     tag "${meta.id}"

micone/pipelines/modules/network_inference/correlation/pearson.nf

@@ -1,3 +1,5 @@
+include { getHierarchy } from ='../../../functions/functions.nf'
+
 process pearson {
     label 'micone'
     tag "${meta.id}"

micone/pipelines/modules/network_inference/correlation/propr.nf

@@ -1,3 +1,5 @@
+include { getHierarchy } from ='../../../functions/functions.nf'
+
 process propr {
     label 'propr'
     tag "${meta.id}"

micone/pipelines/modules/network_inference/correlation/sparcc.nf

@@ -1,3 +1,5 @@
+include { getHierarchy } from ='../../../functions/functions.nf'
+
 process sparcc {
     label 'sparcc'
     tag "${meta.id}"

micone/pipelines/modules/network_inference/correlation/spearman.nf

@@ -1,3 +1,5 @@
+include { getHierarchy } from ='../../../functions/functions.nf'
+
 process spearman {
     label 'micone'
     tag "${meta.id}"

micone/pipelines/modules/network_inference/direct/export_gml.nf

@@ -1,3 +1,5 @@
+include { getHierarchy } from ='../../../functions/functions.nf'
+
 process export_gml {
     label 'flashweave'
     tag "${meta.id}"

micone/pipelines/modules/network_inference/direct/flashweave.nf

@@ -1,3 +1,5 @@
+include { getHierarchy } from ='../../../functions/functions.nf'
+
 process flashweave {
     label 'flashweave'
     tag "${meta.id}"

micone/pipelines/modules/network_inference/direct/mldm.nf

@@ -1,3 +1,5 @@
+include { getHierarchy } from ='../../../functions/functions.nf'
+
 process mldm {
     label 'mldm'
     tag "${meta.id}"

micone/pipelines/modules/network_inference/direct/spieceasi.nf

@@ -1,3 +1,5 @@
+include { getHierarchy } from ='../../../functions/functions.nf'
+
 process spieceasi {
     label 'spieceasi'
     tag "${meta.id}"

micone/pipelines/modules/network_inference/network/make_network_with_pvalue.nf

@@ -1,3 +1,5 @@
+include { getHierarchy } from ='../../../functions/functions.nf'
+
 process make_network_with_pvalue {
     label 'micone'
     tag "${meta.id}"

micone/pipelines/modules/network_inference/network/make_network_without_pvalue.nf

@@ -1,3 +1,5 @@
+include { getHierarchy } from ='../../../functions/functions.nf'
+
 process make_network_without_pvalue {
     label 'micone'
     tag "${meta.id}"

micone/pipelines/modules/otu_processing/export/biom2tsv.nf

@@ -1,3 +1,5 @@
+include { getHierarchy } from ='../../../functions/functions.nf'
+
 process biom2tsv {
     label 'micone'
     tag "${meta.id}"

micone/pipelines/modules/otu_processing/transform/group.nf

@@ -1,3 +1,5 @@
+include { getHierarchy } from ='../../../functions/functions.nf'
+
 process group {
     label 'micone'
     tag "${meta.id}:${tax_level}"

micone/pipelines/modules/otu_processing/transform/normalize.nf

@@ -1,3 +1,5 @@
+include { getHierarchy } from ='../../../functions/functions.nf'
+
 process normalize {
     label 'micone'
     tag "${meta.id}"

micone/pipelines/modules/tax_assignment/assign/add_md2biom.nf

@@ -1,3 +1,5 @@
+include { getHierarchy } from ='../../../functions/functions.nf'
+
 // Attach the observation and sample metadata to the OTU table
 process add_md2biom {
     label 'qiime2'