Merge pull request #74 from rki-mf1/MarieLataretu/issue72

Marie lataretu/issue72
rki-mf1 · Apr 24, 2024 · f50080f · f50080f
2 parents 453eb8f + 04ace25
commit f50080f
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,13 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.5.2] 2024-04-24
+
+### Fixed
+
+- fixed a bug in the `sc2rf` tables that can crash the HTML summary report
+  - see [#71](https://github.com/rki-mf1/CoVpipe2/issues/71) and [#72](https://github.com/rki-mf1/CoVpipe2/issues/72)
+
 ## [0.5.1] 2024-03-15
 
 ### Added

diff --git a/bin/summary_report.Rmd b/bin/summary_report.Rmd
@@ -101,7 +101,7 @@ dt.president_results <- as.data.table(ldply(params$president_results, fread, sep
 dt.pangolin_results <- as.data.table(ldply(params$pangolin_results, fread))
 dt.nextclade_results <- as.data.table(ldply(params$nextclade_results, fread, sep='\t'))
 dt.sc2rf_results <- as.data.table(ldply(params$sc2rf_results, fread, sep=','))
-names(dt.sc2rf_results) <- c('sample','examples','intermissions','breakpoints','regions')
+names(dt.sc2rf_results) <- c('sample','examples','intermissions','breakpoints','regions','unique_subs','alleles')
 if(params$vois_results != 'none'){
   dt.vois_results <- as.data.table(ldply(params$vois_results, fread))
 }

diff --git a/modules/sc2rf.nf b/modules/sc2rf.nf
@@ -23,13 +23,13 @@ process sc2rf {
     if [[ \$(wc -l <${name}_sc2rf.csv) -eq 0 ]] 
     then
         # add empty csv line, if no output at all (e.g. script teminates with parameter problem, but exits with 0)
-        echo ${name},,,, >> ${name}_sc2rf.csv
+        echo ${name},,,,,, >> ${name}_sc2rf.csv
     elif [[ \$(wc -l <${name}_sc2rf.csv) -eq 1 ]] 
     then
         # only header as output
         # remove header because of weired newline character after header that breaks the R report
         # overwrite with empty csv line
-        echo ${name},,,, > ${name}_sc2rf.csv
+        echo ${name},,,,,, > ${name}_sc2rf.csv
     else
         # remove header because of weired newline character after header that breaks the R report
         sed -i 1d ${name}_sc2rf.csv

diff --git a/tests/test.yml b/tests/test.yml
@@ -132,7 +132,7 @@
       md5sum: fcf7e3bc0b3c852a08a8ba801c406920
     - path: "results/Report/single_tables/president_results.tsv"
     - path: "results/Report/single_tables/sc2rf_results.csv"
-      md5sum: d02d8ab1b54d11b1aa16edc719b75796
+      md5sum: 5b14f5ad4a6ffd092c351f6260e3fade
 
 - name: test-update
   command: nextflow run ./CoVpipe2.nf -c ./tests/nextflow.config -profile local --update
@@ -267,4 +267,4 @@
     - path: "results/Report/single_tables/pangolin_results.csv"
     - path: "results/Report/single_tables/president_results.tsv"
     - path: "results/Report/single_tables/sc2rf_results.csv"
-      md5sum: d02d8ab1b54d11b1aa16edc719b75796
+      md5sum: 5b14f5ad4a6ffd092c351f6260e3fade