Rmarkdown report fails: Detected 7 column names but the data has 5 co…

…lumns Fixes #72
rki-mf1 · Apr 24, 2024 · bdc0ee4 · bdc0ee4
1 parent 453eb8f
commit bdc0ee4
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Showing 2 changed files with 3 additions and 3 deletions.
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