Add G to ntLink_rounds command to avoid parameter name collision (#145)

* Add G to ntLink_rounds command to avoid parameter name collision

* Also specify 'a' for ntLink

* A collision, but happened to be same default for goldrush-path and ntLink
* Specify it for ntLink just to be safe

Author: lcoombe

bin/goldrush

@@ -288,9 +288,9 @@ $(p2).$(polished_infix).span$(span).dist$(dist).tigmint.fa: $(p2).$(polished_inf
 ntLink_all_rounds: $(p2).$(polished_infix).span$(span).dist$(dist).tigmint.fa.k$(k_ntLink).w$(w_ntLink).z$z.ntLink.gap_fill.$(rounds)rounds.fa check-G check-reads
 
 %.fa.k$(k_ntLink).w$(w_ntLink).z$z.ntLink.gap_fill.$(rounds)rounds.fa: %.fa $(long_reads)
-	$(time) ntLink_rounds run_rounds_gaps target=$< t=$t k=$(k_ntLink) w=$(w_ntLink) z=$z soft_mask=$(soft_mask) rounds=$(rounds) reads=$(long_reads)
+	$(time) ntLink_rounds run_rounds_gaps target=$< t=$t k=$(k_ntLink) w=$(w_ntLink) z=$z soft_mask=$(soft_mask) rounds=$(rounds) reads=$(long_reads) G=-1 a=1
 ifneq ($(dev), True)
-	ntLink_rounds clean target=$< t=$t k=$(k_ntLink) w=$(w_ntLink) z=$z soft_mask=$(soft_mask) rounds=$(rounds) reads=$(long_reads)
+	ntLink_rounds clean target=$< t=$t k=$(k_ntLink) w=$(w_ntLink) z=$z soft_mask=$(soft_mask) rounds=$(rounds) reads=$(long_reads) G=-1 a=1
 endif
 
 ntLink_softlink: $(p2).$(polished_infix).span$(span).dist$(dist).tigmint.fa.k$(k_ntLink).w$(w_ntLink).ntLink-$(rounds)rounds.fa check-G check-reads