Merge pull request nf-core#170 from mirpedrol/r-script-bug

remove patterns from correct_insertion_vc
LaurenceKuhl · Jul 9, 2024 · a4e18cf · a4e18cf
2 parents d94bab6 + 42b1fc0
commit a4e18cf
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Fix singularity image pull tag for MAGeCKFlute ([#160](https://github.com/nf-core/crisprseq/pull/160))
 - Skip dolar signs on containerOptions ([#163](https://github.com/nf-core/crisprseq/pull/163))
+- Fix error in R script when adding patterns ([#170](https://github.com/nf-core/crisprseq/pull/170))
 
 ### Deprecated
 

diff --git a/bin/cigar_parser.R b/bin/cigar_parser.R
@@ -772,7 +772,7 @@ ref_fasta = opt$reference
 gRNA_sequence = opt$gRNA_sequence
 sample_id = opt$sample_name
 temp = opt$template
-spikes = opt$spikes ### yes or no
+spikes = opt$spikes
 files_summary = opt$summary_file
 cut_pos_prot = as.numeric(opt$cut_site)
 mock = opt$mock
@@ -900,6 +900,7 @@ if (dim(alignment_info)[1] != 0){
             separated_indels["post_ins_nt"]<-NA
         }else if(dim(separated_indels_ins_all)[1]>0){
             separated_indels <- separated_indels_ins_all
+            separated_indels["patterns"]<-NA
         }