Merge pull request #74 from mirpedrol/more-report-plots

Add more report plots
nf-core · Sep 28, 2023 · 4fcf214 · 4fcf214
2 parents 2aabcf5 + 10c7c74
commit 4fcf214
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Showing 7 changed files with 734 additions and 10 deletions.
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/crisprseq" target="_blank">nf-core/crisprseq</a>
+  This report has been generated by the <a href="https://github.com/nf-core/crisprseq/releases/tag/dev" target="_blank">nf-core/crisprseq</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/crisprseq/2.0.0/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/crisprseq/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-crisprseq-methods-description":
     order: -1000

diff --git a/bin/cigar_parser.R b/bin/cigar_parser.R
@@ -946,7 +946,8 @@ if (dim(alignment_info)[1] != 0){
         dels <- separated_indels %>% filter(Modification == "del")
         dels_count <- dim(dels)[1]
         if ( t_type == "dels-out" || t_type == "dels-in"){
-            dels_count <- dels_count - t_reads
+            t_in_dels <- dels %>% filter(Ids %in% t_ids[[1]])
+            dels_count <- dels_count - dim(t_in_dels)[1]
         }
         ins <- separated_indels %>% filter(Modification == "ins")
         ins_count <- dim(ins)[1]