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Use vg sim command instead of vg-toil sim
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@susannamorin
susannamorin committed Apr 1, 2021
1 parent f33c41d commit 21027b8
Showing 1 changed file with 4 additions and 4 deletions.
8 changes: 4 additions & 4 deletions scripts/mcmc_Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -52,8 +52,8 @@ $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_0).vg: $(TOIL_OS)/$(BASENAME)_$(HA
$(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_0).xg: $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_0).vg
vg index -x $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_0).xg $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_0).vg

$(TOIL_OS)/$(BASENAME)_$(HAPLO_0).gam: $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_0).xg
toil-vg sim --gam --sim_opts '--sub-rate 0.1 --indel-rate 0.1 --read-length 100' --container None --out_name $(BASENAME)_$(HAPLO_0) $(TOIL_JS) $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_0).xg $(READS) $(TOIL_OS)
$(TOIL_OS)/$(BASENAME)_$(HAPLO_0).gam: $(TOIL_OS)/$(BASENAME).xg $(TOIL_OS)/$(BASENAME).gbwt
vg sim -x $(TOIL_OS)/$(BASENAME).xg -g $(TOIL_OS)/$(BASENAME).gbwt -m $(SAMP) -n 300 --sub-rate 0.05 --indel-rate 0.05 --read-length 100 -a > $(TOIL_OS)/$(BASENAME)_$(HAPLO_0).gam

$(TOIL_OS)/$(BASENAME)_$(HAPLO_1)_thread.merge.vg: $(TOIL_OS)/$(BASENAME).vg $(TOIL_OS)/$(BASENAME).gbwt $(TOIL_OS)/$(BASENAME).xg
vg paths -d -v $(TOIL_OS)/$(BASENAME).vg > $(TOIL_OS)/$(BASENAME)_$(HAPLO_1)_thread.merge.vg
Expand All @@ -65,8 +65,8 @@ $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_1).vg: $(TOIL_OS)/$(BASENAME)_$(HA
$(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_1).xg: $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_1).vg
vg index -x $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_1).xg $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_1).vg

$(TOIL_OS)/$(BASENAME)_$(HAPLO_1).gam: $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_1).xg
toil-vg sim --gam --sim_opts '--sub-rate 0.1 --indel-rate 0.1 --read-length 100' --container None --out_name $(BASENAME)_$(HAPLO_1) $(TOIL_JS) $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_1).xg $(READS) $(TOIL_OS)
$(TOIL_OS)/$(BASENAME)_$(HAPLO_1).gam: $(TOIL_OS)/$(BASENAME).xg $(TOIL_OS)/$(BASENAME).gbwt
vg sim -x $(TOIL_OS)/$(BASENAME).xg -g $(TOIL_OS)/$(BASENAME).gbwt -m $(SAMP) -n 300 --sub-rate 0.05 --indel-rate 0.05 --read-length 100 -a > $(TOIL_OS)/$(BASENAME)_$(HAPLO_1).gam

$(TOIL_OS)/$(BASENAME)_merged.gam: $(TOIL_OS)/$(BASENAME)_$(HAPLO_0).gam $(TOIL_OS)/$(BASENAME)_$(HAPLO_1).gam
cat $(TOIL_OS)/$(BASENAME)_$(HAPLO_0).gam $(TOIL_OS)/$(BASENAME)_$(HAPLO_1).gam > $(TOIL_OS)/$(BASENAME)_merged.gam
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@adamnovak
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vg CI tests complete for branch min-cut-graph. View the full report here.

15 tests passed, 0 tests failed and 0 tests skipped in 9389 seconds

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