Fix: Typo identified while testing

segrelab · May 26, 2021 · 59fa24e · 59fa24e
1 parent bda0e99
commit 59fa24e
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Showing 8 changed files with 19 additions and 18 deletions.
diff --git a/micone/pipelines/modules/denoise_cluster/chimera_checking/remove_bimera_workflow.nf b/micone/pipelines/modules/denoise_cluster/chimera_checking/remove_bimera_workflow.nf
@@ -1,6 +1,6 @@
 include { create_seqtable } from './create_seqtable.nf'
 include { remove_bimera } from './remove_bimera.nf'
-include { hashing3 } from './../denoise_cluster/hashing3.nf'
+include { hashing3 } from './../otu_assignment/hashing3.nf'
 
 
 workflow remove_bimera_workflow {

diff --git a/micone/pipelines/modules/denoise_cluster/otu_assignment/de_novo.nf b/micone/pipelines/modules/denoise_cluster/otu_assignment/de_novo.nf
@@ -1,6 +1,6 @@
 // Step2: de_novo OTU picking
 process de_novo {
-    lable 'qiime1'
+    label 'qiime1'
     tag "${meta.id}"
     input:
         tuple val(meta), file(fasta_file)

diff --git a/micone/pipelines/modules/denoise_cluster/otu_assignment/open_reference_workflow.nf b/micone/pipelines/modules/denoise_cluster/otu_assignment/open_reference_workflow.nf
@@ -3,7 +3,7 @@ include { open_reference } from './open_reference.nf'
 include { hashing2 } from './hashing2.nf'
 
 
-workflow de_novo_workflow {
+workflow open_reference_workflow {
     take:
         // tuple val(id), file(sequence_files), file(manifest_file)
         input_channel

diff --git a/...pipelines/modules/denoise_cluster/sequence_processing/demultiplexing_illumina_workflow.nf b/...pipelines/modules/denoise_cluster/sequence_processing/demultiplexing_illumina_workflow.nf
@@ -1,5 +1,5 @@
-include { import_sequences_sh } from './import_sequences_sh.nf'
-include { demultiplexing_illumina } from './demultiplex_illumina.nf'
+include { import_sequences } from './import_sequences_sh.nf'
+include { demultiplexing_illumina } from './demultiplexing_illumina.nf'
 include { export_sequences } from './export_sequences.nf'
 
 
@@ -9,7 +9,7 @@ workflow demultiplexing_illumina_workflow {
         input_channel
     main:
         input_channel \
-            | import_sequences_sh \
+            | import_sequences \
             | demultiplexing_illumina \
             // | join_reads \
             | export_sequences

diff --git a/micone/pipelines/modules/denoise_cluster/sequence_processing/trim_filter_fixed_workflow.nf b/micone/pipelines/modules/denoise_cluster/sequence_processing/trim_filter_fixed_workflow.nf
@@ -1,4 +1,4 @@
-include { import_sequences_py } from './import_sequences_py.nf'
+include { import_sequences } from './import_sequences_py.nf'
 include { export_visualization } from './export_visualization.nf'
 include { quality_analysis } from './quality_analysis.nf'
 include { trimming } from './trimming.nf'
@@ -10,7 +10,7 @@ workflow trim_filter_fixed_workflow {
         input_channel
     main:
         input_channel \
-            | import_sequences_py \
+            | import_sequences \
             | export_visualization \
             | quality_analysis \
             | join(input_channel) \

diff --git a/micone/pipelines/modules/network_inference/network_inference_workflow.nf b/micone/pipelines/modules/network_inference/network_inference_workflow.nf
@@ -13,13 +13,14 @@ include { flashweave_workflow } from './direct/flashweave_workflow.nf'
 include { mldm_workflow } from './direct/mldm_workflow.nf'
 
 // Network imports
-include { make_network } from './network/make_network.nf'
+include { make_network_with_pvalue } from './network/make_network_with_pvalue.nf'
+include { make_network_without_pvalue } from './network/make_network_without_pvalue.nf'
 
 // Main workflow
 workflow network_inference_workflow {
     take:
-        // tuple val(meta), file(otu_file), file(obs_metadata), file(sample_metadata), file(children_map)
-        input_channel
+    // tuple val(meta), file(otu_file), file(obs_metadata), file(sample_metadata), file(children_map)
+    input_channel
 
     main:
     input_channel \
@@ -31,24 +32,24 @@ workflow network_inference_workflow {
             & flashweave_workflow \
             & mldm_workflow )
 
-    // NOTE: These will have have extra pvalues
+    // NOTE: These will have have extra pvalue
     corr_output = sparcc_workflow.out
                     .mix(
                         pearson_workflow.out,
                         spearman_workflow.out,
                         propr_workflow.out,
                     )
-    // NOTE: These will not have pvalues
+    // NOTE: These will not have pvalue
     direct_output = spieceasi_workflow.out
                         .mix(
                             flashweave_workflow.out,
                             mldm_workflow.out
                         )
 
-    make_network_with_pvalues(corr_output)
-    make_network_without_pvalues(direct_output)
+    make_network_with_pvalue(corr_output)
+    make_network_without_pvalue(direct_output)
 
-    network_channel = make_network_with_pvalues.out.mix(make_network_without_pvalues)
+    network_channel = make_network_with_pvalue.out.mix(make_network_without_pvalue.out)
 
     emit:
         // all processes have publishDir

diff --git a/micone/pipelines/modules/tax_assignment/assign/naive_bayes_workflow.nf b/micone/pipelines/modules/tax_assignment/assign/naive_bayes_workflow.nf
@@ -3,7 +3,7 @@ include { add_md2biom } from './add_md2biom.nf'
 
 // NOTE: We try to simplify the workflow by requiring the user to pre-train the classifier
 
-workflow blast_workflow {
+workflow naive_bayes_workflow {
     take:
         // tuple val(meta), file('otu_table.biom'), file('rep_seqs.fasta'), file(samplemetadata_files)
         input_channel

diff --git a/micone/pipelines/modules/tax_assignment/tax_assignment_workflow.nf b/micone/pipelines/modules/tax_assignment/tax_assignment_workflow.nf
@@ -12,7 +12,7 @@ workflow tax_assignment_workflow {
         input_channel
     main:
         input_channel \
-            | (naive_bayes_workflow & blast_workflow) \
+            | (naive_bayes_workflow & blast_workflow)
         output_channel = blast_workflow.out
                             .mix(naive_bayes_workflow.out)
     emit: