Merge pull request #66 from mirpedrol/fix-resume-modules

Fix resume

CHANGELOG.md

@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+- 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))
 
 ### Deprecated

modules/local/alignment_summary.nf

@@ -11,7 +11,7 @@ process ALIGNMENT_SUMMARY {
     tuple val(meta), path(reads), path(summary)
 
     output:
-    tuple val(meta), path(summary), emit: summary
+    tuple val(meta), path("*_alignment_summary.csv"), emit: summary
 
     when:
     task.ext.when == null || task.ext.when

modules/local/clustering_summary.nf

@@ -11,7 +11,7 @@ process CLUSTERING_SUMMARY {
     tuple val(meta), path(reads), path(summary)
 
     output:
-    tuple val(meta), path(summary), emit: summary
+    tuple val(meta), path("*_clustering_summary.csv"), emit: summary
 
     when:
     task.ext.when == null || task.ext.when

modules/local/merging_summary.nf

@@ -12,7 +12,7 @@ process MERGING_SUMMARY {
 
 
     output:
-    tuple val(meta), path("*_summary.csv"), emit: summary
+    tuple val(meta), path("*_merging_summary.csv"), emit: summary
 
     when:
     task.ext.when == null || task.ext.when

templates/alignment_summary.py

@@ -12,7 +12,8 @@
     summary_lines = summary.readlines()
 
 add_line = True
-with open("$summary", "w") as output_file:
+outname = "$summary".replace("_clustering_summary.csv", "_alignment_summary.csv")
+with open(outname, "w") as output_file:
     for line in summary_lines:
         if "aligned-reads" not in line:
             output_file.write(line)

templates/clustering_summary.py

@@ -12,7 +12,8 @@
     summary_lines = summary.readlines()
 
 add_line = True
-with open("$summary", "w") as output_file:
+outname = "$summary".replace("_merging_summary.csv", "_clustering_summary.csv")
+with open(outname, "w") as output_file:
     for line in summary_lines:
         if "clustered-reads" not in line:
             output_file.write(line)

templates/merging_summary.py

@@ -34,7 +34,7 @@
 else:
     prefix = "$meta.id"
 
-with open(f"{prefix}_summary.csv", "w") as output_file:
+with open(f"{prefix}_merging_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(