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Add more report plots #74

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merged 10 commits into from
Sep 28, 2023
Merged

Add more report plots #74

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54f65fe
add R script to generate more output plots (some modifications from o…
mirpedrol Aug 18, 2023
c546e54
save plot results in a folder called plots
mirpedrol Aug 18, 2023
7ea4c31
print plotted percentage in substitution percentage plot
mirpedrol Aug 21, 2023
4acfc21
add mulled container for crisprseq_plotter
mirpedrol Aug 22, 2023
a6cfae3
fix left-padding spaces
mirpedrol Aug 22, 2023
2514145
output empty *_delAlleles_plot.png image when required
mirpedrol Aug 22, 2023
08334c0
output empty *_subs-perc_plot_LOGO.png image when required
mirpedrol Aug 22, 2023
69ddf24
Apply suggestions from code review
mirpedrol Sep 28, 2023
79e8269
fix multiqc_config.yml
mirpedrol Sep 28, 2023
10c7c74
fix multiqc_config.yml linting test
mirpedrol Sep 28, 2023
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4 changes: 2 additions & 2 deletions assets/multiqc_config.yml
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Original file line number Diff line number Diff line change
@@ -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
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3 changes: 2 additions & 1 deletion bin/cigar_parser.R
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Expand Up @@ -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]
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