Rename merging summary

CHANGELOG.md

@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Summary processes don't modify the input file anymore, allowing resuming these processes ([#66](https://github.com/nf-core/crisprseq/pull/66))
 - Do not stash unexistent files, use empty lists instead. Fixes AWS tests ([#67](https://github.com/nf-core/crisprseq/pull/67))
+- Rename process `merging_summary` to `preprocessing_summary` to improve clarity ([#69](https://github.com/nf-core/crisprseq/pull/69))
 
 ### Deprecated
 

conf/modules.config

@@ -128,7 +128,7 @@ process {
         ext.prefix = { "${fasta.baseName}_top" }
     }
 
-    withName: MERGING_SUMMARY {
+    withName: PREPROCESSING_SUMMARY {
         publishDir = [
             path: { "${params.outdir}/summary/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
             mode: params.publish_dir_mode,

modules/local/merging_summary.nf → modules/local/preprocessing_summary.nf

@@ -1,4 +1,4 @@
-process MERGING_SUMMARY {
+process PREPROCESSING_SUMMARY {
     tag "$meta.id"
     label 'process_single'
 
@@ -12,11 +12,11 @@ process MERGING_SUMMARY {
 
 
     output:
-    tuple val(meta), path("*_merging_summary.csv"), emit: summary
+    tuple val(meta), path("*_preprocessing_summary.csv"), emit: summary
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    template 'merging_summary.py'
+    template 'preprocessing_summary.py'
 }

templates/clustering_summary.py

@@ -12,7 +12,7 @@
     summary_lines = summary.readlines()
 
 add_line = True
-outname = "$summary".replace("_merging_summary.csv", "_clustering_summary.csv")
+outname = "$summary".replace("_preprocessing_summary.csv", "_clustering_summary.csv")
 with open(outname, "w") as output_file:
     for line in summary_lines:
         if "clustered-reads" not in line:

templates/merging_summary.py → templates/preprocessing_summary.py

@@ -34,7 +34,7 @@
 else:
     prefix = "$meta.id"
 
-with open(f"{prefix}_merging_summary.csv", "w") as output_file:
+with open(f"{prefix}_preprocessing_summary.csv", "w") as output_file:
     output_file.write("class, count\\n")
     output_file.write(f"raw-reads, {raw_reads_count} (100.0%)\\n")
     output_file.write(

workflows/crisprseq_targeted.nf

@@ -38,14 +38,14 @@ ch_multiqc_custom_methods_description = params.multiqc_methods_description ? fil
 //
 // MODULE
 //
-include { FIND_ADAPTERS      } from '../modules/local/find_adapters'
-include { EXTRACT_UMIS       } from '../modules/local/extract_umis'
-include { ORIENT_REFERENCE   } from '../modules/local/orient_reference'
-include { CIGAR_PARSER       } from '../modules/local/cigar_parser'
-include { MERGING_SUMMARY    } from '../modules/local/merging_summary'
-include { CLUSTERING_SUMMARY } from '../modules/local/clustering_summary'
-include { ALIGNMENT_SUMMARY  } from '../modules/local/alignment_summary'
-include { TEMPLATE_REFERENCE } from '../modules/local/template_reference'
+include { FIND_ADAPTERS         } from '../modules/local/find_adapters'
+include { EXTRACT_UMIS          } from '../modules/local/extract_umis'
+include { ORIENT_REFERENCE      } from '../modules/local/orient_reference'
+include { CIGAR_PARSER          } from '../modules/local/cigar_parser'
+include { PREPROCESSING_SUMMARY } from '../modules/local/preprocessing_summary'
+include { CLUSTERING_SUMMARY    } from '../modules/local/clustering_summary'
+include { ALIGNMENT_SUMMARY     } from '../modules/local/alignment_summary'
+include { TEMPLATE_REFERENCE    } from '../modules/local/template_reference'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -347,7 +347,7 @@ workflow CRISPRSEQ_TARGETED {
                 }
                 return [ meta, reads, assembled, masked, trimmed ]
             }
-            .set { ch_merging_summary_data }
+            .set { ch_preprocessing_summary_data }
     } else {
         ch_cat_fastq.paired
             .mix(ch_cat_fastq.single)
@@ -359,14 +359,14 @@ workflow CRISPRSEQ_TARGETED {
                 }
                 return [ meta, reads, assembled, masked, [] ]
             }
-            .set { ch_merging_summary_data }
+            .set { ch_preprocessing_summary_data }
     }
 
     //
     // MODULE: Summary of merged reads
     //
-    MERGING_SUMMARY {
-        ch_merging_summary_data
+    PREPROCESSING_SUMMARY {
+        ch_preprocessing_summary_data
     }
 
 
@@ -587,7 +587,7 @@ workflow CRISPRSEQ_TARGETED {
     //
     CLUSTERING_SUMMARY (
         ch_preprocess_reads
-            .join(MERGING_SUMMARY.out.summary)
+            .join(PREPROCESSING_SUMMARY.out.summary)
     )