No PTM in any set was always triggered, because of the pipefail optio…

…n in NF, so make it an explicit if statement

bin/qc_protein.R

@@ -247,8 +247,8 @@ if (feattype != 'peptides') {
 
 # precursorarea
 precursorcols = c(featcol, colnames(feats)[grep('area', colnames(feats))])
-anyrowsms1 = nrow(feats[rowSums(is.na(feats[,precursorcols])) != length(precursorcols),])
 if (length(precursorcols) > 1) {
+    anyrowsms1 = nrow(feats[rowSums(is.na(feats[,precursorcols])) != length(precursorcols),])
     svg('precursorarea', height=(nrsets + 1), width=width)
     if (anyrowsms1) {
       parea = melt(feats, id.vars=featcol, na.rm=T, measure.vars = precursorcols[2:length(precursorcols)])

main.nf

@@ -1301,7 +1301,10 @@ process createPTMLookup {
   msstitch split -i "${ptmtable}" --splitcol bioset
   ${setnames.collect() { "test -f '${it}.tsv' || echo 'No PTMs found for set ${it}' >> warnings" }.join(' && ') }
   # No PTMs at all overwrites the per-set messages
-  tail -n+2 ${ptmtable} | head | grep . >/dev/null || echo 'No PTMs found in any set' > warnings
+  if [[ \$(wc -l <ptm_psmtable.txt) -lt 2 ]]
+  then
+    echo 'No PTMs found in any set' > warnings
+  fi
   """
 }