Merge pull request #138 from mirpedrol/fix-parser-error

create empty -QC-indels.csv file if alignments not found - fix AWS megatests

CHANGELOG.md

@@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed
 
 - Adapt cutadapt module to work with single-end and paired-end reads again ([#121](https://github.com/nf-core/crisprseq/pull/121))
+- Create empty \*-QC-indels.csv file if alignments not found. ([#138](https://github.com/nf-core/crisprseq/pull/138))
 
 ## [v2.1.1 - Jamon Salas - patch](https://github.com/nf-core/crisprseq/releases/tag/2.1.1) - [14.12.2023]
 

bin/cigar_parser.R

@@ -1234,4 +1234,10 @@ if (dim(alignment_info)[1] != 0){
     colnames(edit_summary_perc)[1] = results_path # Rename the column to add the sample ID
     edit_summary_perc <- t(edit_summary_perc) # t() will add classes as columns and counts as values, 1 row per sample
     write.csv(edit_summary_perc,file=paste0(results_path, "_edits.csv"))
+    indel_filters
+    prevc_classes_mqc <- c("Wt passing filter", "Wt NOT passing filter", "Indels NOT passing filter",
+            "Above error & in pick", "NOT above error & in pick", "NOT above error & NOT in pick", "Above error & NOT in pick")
+    prevc_counts_mqc <- c(0, 0, 0, 0, 0, 0, 0)
+    indel_filters <- data.frame(sample = unlist(prevc_counts_mqc), row.names = unlist(prevc_classes_mqc))
+    write.csv(indel_filters,file=paste0(results_path, "_QC-indels.csv"))
 }