bunch of hacks for control flow

main.nf

@@ -194,6 +194,9 @@ process RepeatMasker1 {
   set age, 'seqfile.outinner.out', 'seqfile.outinner.masked' into repeatMasker1Unclean
 
   """
+# only run RepeatMasker if the previous processes have found anything, i.e. there is something in their output file 
+if [[ `wc -l repeats_to_mask_LTR.fasta | cut -c 1` != "0" ]]; then  
+
 RepeatMasker \
  -lib repeats_to_mask_LTR.fasta \
  -nolow \
@@ -203,6 +206,10 @@ RepeatMasker \
 
 if [ ! -f seqfile.outinner.masked ]; then
   cp seqfile.outinner seqfile.outinner.masked
+fi
+
+#otherwise create empty dummy files in order for following processes not to crash
+else touch seqfile.outinner.masked seqfile.outinner.out;
 fi
   """
 }
@@ -251,6 +258,12 @@ outinner_blastx_parse.pl \
 
 if [ ! -s passed_outinner_sequence.fasta ]; then
   echo -e '>dummy empty sequence\nACTACTAC' > passed_outinner_sequence.fasta
+fi
+#this follows on from above, if 'old' or 'new' did not find anything, a dummy file needs to be created 
+#in order for following processes not to crash
+
+if [[ `wc -l passed_outinner_sequence.fasta | cut -c 1` == "0" ]]; then
+  echo -e '>dummy empty sequence\nACTACTAC' > passed_outinner_sequence.fasta
 fi
   """
 }
@@ -273,6 +286,9 @@ process buildExemplars {
   set age, 'LTR.lib' into exemplars
 
   """
+#Only run the scripts if previous processes found something, otherwise don't bother and create a dummy file
+if [[ `wc -l CRL_Step3_Passed_Elements.fasta | cut -c 1` != "0" ]]; then  
+
 CRL_Step4.pl \
  --step3 CRL_Step3_Passed_Elements.fasta \
  --resultfile seqfile.result \
@@ -297,6 +313,12 @@ CRL_Step5.pl \
  --final LTR.lib \
  --pcoverage 90 \
  --pidentity 80
+
+#This file needs to have at least one entry, hence the dummy entry, otherwise the pipeline crashes.
+#I am however not sure if this dummy sequence will influence anything else downstream and it may have
+#to be dealt with later
+else echo -e '>dummy empty sequence\nACTACTAC' > LTR.lib;
+fi
   """
 }