From 265efd714d614704b2d0f5427e52f45bd6e57c2b Mon Sep 17 00:00:00 2001 From: Lauren Coombe Date: Wed, 6 Dec 2023 10:03:17 -0800 Subject: [PATCH] Fix arcs-tigmint rule in arcs-make (#165) * Fix Tigmint call in arcs-make arcs-tigmint rule * Fix whitespace --- ...t250_s70_r0.05_e30000_z500_l3_a0.9.tigpair_checkpoint.tsv | 5 ++++- bin/arcs-make | 2 +- 2 files changed, 5 insertions(+), 2 deletions(-) mode change 120000 => 100644 Examples/arcs-long_test-demo/output/test_scaffolds_c3_m8-10000_cut250_s70_r0.05_e30000_z500_l3_a0.9.tigpair_checkpoint.tsv diff --git a/Examples/arcs-long_test-demo/output/test_scaffolds_c3_m8-10000_cut250_s70_r0.05_e30000_z500_l3_a0.9.tigpair_checkpoint.tsv b/Examples/arcs-long_test-demo/output/test_scaffolds_c3_m8-10000_cut250_s70_r0.05_e30000_z500_l3_a0.9.tigpair_checkpoint.tsv deleted file mode 120000 index 815608f..0000000 --- a/Examples/arcs-long_test-demo/output/test_scaffolds_c3_m8-10000_cut250_s70_r0.05_e30000_z500_l3_a0.9.tigpair_checkpoint.tsv +++ /dev/null @@ -1 +0,0 @@ -test_scaffolds_c3_m8-10000_cut250_s70_r0.05_e30000_z500.tigpair_checkpoint.tsv \ No newline at end of file diff --git a/Examples/arcs-long_test-demo/output/test_scaffolds_c3_m8-10000_cut250_s70_r0.05_e30000_z500_l3_a0.9.tigpair_checkpoint.tsv b/Examples/arcs-long_test-demo/output/test_scaffolds_c3_m8-10000_cut250_s70_r0.05_e30000_z500_l3_a0.9.tigpair_checkpoint.tsv new file mode 100644 index 0000000..1a2dfcb --- /dev/null +++ b/Examples/arcs-long_test-demo/output/test_scaffolds_c3_m8-10000_cut250_s70_r0.05_e30000_z500_l3_a0.9.tigpair_checkpoint.tsv @@ -0,0 +1,4 @@ +10 f1 r2 5 500 +10 f2 r1 5 500 +10 r2 r3 4 400 +10 f3 f2 4 400 diff --git a/bin/arcs-make b/bin/arcs-make index c2da415..4cfcb84 100755 --- a/bin/arcs-make +++ b/bin/arcs-make @@ -222,7 +222,7 @@ arks-tigmint: tigmint arks-with-tigmint tigmint: $(draft).tigmint.fa # Run tigmint $(draft).tigmint.fa: $(draft).fa $(reads).fq.gz - $(gtime) tigmint tigmint draft=$(draft) reads=$(reads) minsize=$(minsize) as=$(as) nm=$(nm) dist=$(dist) mapq=$(mapq) trim=$(trim) span=$(span) window=$(window) t=$t + $(gtime) tigmint-make tigmint draft=$(draft) reads=$(reads) minsize=$(minsize) as=$(as) nm=$(nm) dist=$(dist) mapq=$(mapq) trim=$(trim) span=$(span) window=$(window) t=$t #Pre-processing long reads; cut into shorter segments (pseudo-linked reads) $(reads).cut$(cut).fq.gz: $(long_reads)