Quote filenames with spaces accoding to #nexflow-io/nextf4240 , which…

… here means assuring they are from a list in mergePTMs

main.nf

@@ -1346,10 +1346,12 @@ process mergePTMPeps {
   script:
   peptable = params.totalproteomepsms ? 'ptm_peptides_total_proteome_adjusted.txt' : 'ptm_peptides_not_adjusted.txt'
   peptable_no_adjust = 'ptm_peptides_not_adjusted.txt'
+  listpeptides = listify(peptides)
+  listnotp_adj = listify(notp_adjust_peps)
   """
   cat ptmlup.sql > pepptmlup.sql
   # Create first table, input for which is either adjusted or not
-  msstitch merge -i ${peptides.collect() { "$it" }.join(' ')} --setnames ${setnames.collect() { "'$it'" }.join(' ')} --dbfile pepptmlup.sql -o mergedtable --no-group-annotation \
+  msstitch merge -i ${listpeptides.collect() { "$it" }.join(' ')} --setnames ${setnames.collect() { "'$it'" }.join(' ')} --dbfile pepptmlup.sql -o mergedtable --no-group-annotation \
     --fdrcolpattern '^q-value' --pepcolpattern 'peptide PEP' --flrcolpattern 'FLR' \
     ${!params.noquant && !params.noms1quant ? "--ms1quantcolpattern area" : ''} \
     ${!params.noquant && setisobaric ? "--isobquantcolpattern plex" : ''}
@@ -1360,7 +1362,7 @@ process mergePTMPeps {
     join -j1 -o auto -t '\t' <(paste geneprots <(cut -f3 geneprots | tr -dc ';\\n'| awk '{print length+1}')) <(tail -n+2 mergedtable | sort -k1b,1) >> ${peptable}""" : "mv mergedtable ${peptable}"}
 
   # If total-proteome quant adjustment input was used above, create a second merged NON-adjusted peptide tables
-  ${params.totalproteomepsms ?  "msstitch merge -i ${notp_adjust_peps.collect() { "$it" }.join(' ')} --setnames ${setnames.collect() { "'$it'" }.join(' ')} \
+  ${params.totalproteomepsms ?  "msstitch merge -i ${listnotp_adj.collect() { "$it" }.join(' ')} --setnames ${setnames.collect() { "'$it'" }.join(' ')} \
     --dbfile pepptmlup.sql -o mergedtable --no-group-annotation \
     --fdrcolpattern '^q-value' --pepcolpattern 'peptide PEP' --flrcolpattern 'FLR' \
     ${!params.noquant && !params.noms1quant ? "--ms1quantcolpattern area" : ''} \