don't stash unexistent files, use empty lists instead, fix AWS tests

nf-core · Aug 3, 2023 · 1d111f9 · 1d111f9
1 parent 8dbbcfd
commit 1d111f9
Show file tree

Hide file tree

Showing 3 changed files with 17 additions and 13 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -12,6 +12,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+- Do not stash unexistent files, use empty lists instead. Fixes AWS tests ([#67](https://github.com/nf-core/crisprseq/pull/67))
+
 ### Deprecated
 
 ## [v2.0.0 - Paprika Lovelace](https://github.com/nf-core/crisprseq/releases/tag/2.0.0) - [05.07.2023]

diff --git a/templates/merging_summary.py b/templates/merging_summary.py
@@ -7,7 +7,7 @@
 with gzip.open("${raw_reads[0]}", "rt") as handle:
     raw_reads_count = len(list(SeqIO.parse(handle, "fastq")))
 
-if "$assembled_reads" == "null_a":
+if "$assembled_reads" == "":
     assembled_reads_count = 0
 else:
     with gzip.open("$assembled_reads", "rt") as handle:
@@ -16,7 +16,7 @@
 with gzip.open("$trimmed_reads", "rt") as handle:
     trimmed_reads_count = len(list(SeqIO.parse(handle, "fastq")))  # Filtered reads
 
-if "$trimmed_adapters" == "null_t":
+if "$trimmed_adapters" == "":
     adapters_count = 0
     adapters_percentage = "(0.0%)"
 else:
@@ -41,7 +41,7 @@
         f"merged-reads, {assembled_reads_count} ({round(assembled_reads_count * 100 / raw_reads_count,1)}%)\\n"
     )
     output_file.write(f"reads-with-adapters, {adapters_count} {adapters_percentage}\\n")
-    if "$assembled_reads" == "null_a":
+    if "$assembled_reads" == "":
         output_file.write(
             f"quality-filtered-reads, {trimmed_reads_count} ({round(trimmed_reads_count * 100 / raw_reads_count,1)}%)\\n"
         )

diff --git a/workflows/crisprseq_targeted.nf b/workflows/crisprseq_targeted.nf
@@ -341,21 +341,23 @@ workflow CRISPRSEQ_TARGETED {
             .join(PEAR.out.assembled, remainder: true)
             .join(SEQTK_SEQ_MASK.out.fastx)
             .join(CUTADAPT.out.log)
+            .map { meta, reads, assembled, masked, trimmed ->
+                if (assembled == null) {
+                    assembled = []
+                }
+                return [ meta, reads, assembled, masked, trimmed ]
+            }
             .set { ch_merging_summary_data }
     } else {
         ch_cat_fastq.paired
             .mix(ch_cat_fastq.single)
             .join(PEAR.out.assembled, remainder: true)
             .join(SEQTK_SEQ_MASK.out.fastx)
-            .combine(Channel.value("null"))
-            .map { meta, reads, assembled, masked, trimmed ->
+            .map { meta, reads, assembled, masked ->
                 if (assembled == null) {
-                    assembled = file('null_a')
+                    assembled = []
                 }
-                if (trimmed == "null") {
-                    trimmed = file('null_t')
-                }
-                return [ meta, reads, assembled, masked, trimmed ]
+                return [ meta, reads, assembled, masked, [] ]
             }
             .set { ch_merging_summary_data }
     }
@@ -705,13 +707,13 @@ workflow CRISPRSEQ_TARGETED {
         .join(ALIGNMENT_SUMMARY.out.summary)
         .map { meta, reads, index, reference, protospacer, template, template_bam, reference_template, summary ->
             if (template == null) {
-                template = file('null_t')
+                template = []
             }
             if (template_bam == null) {
-                template_bam = file('null_b')
+                template_bam = []
             }
             if (reference_template == null) {
-                reference_template = file('null_r')
+                reference_template = []
             }
             return [meta, reads, index, reference, protospacer, template, template_bam, reference_template, summary]
         }