Rename instances of GoldRush-Edit to GoldPolish (#125)

* switch gr-edit to goldpolish

* fix capitalizations

* Update README.md

* Update README.md

Co-authored-by: Lauren Coombe <lauren.e.coombe@gmail.com>

* rename goldrush_edit_opts

* Update requirements.txt

* Update README.md

---------

Co-authored-by: Lauren Coombe <lauren.e.coombe@gmail.com>

Author: jwcodee

.gitmodules

@@ -1,3 +1,3 @@
-[submodule "subprojects/goldrush-edit"]
-	path = subprojects/goldrush-edit
-	url = https://git@github.com/bcgsc/goldrush-edit
+[submodule "subprojects/goldpolish"]
+	path = subprojects/goldpolish
+	url = https://git@github.com/bcgsc/goldpolish

README.md

@@ -37,12 +37,12 @@ goldrush run reads=reads G=gsize
 
         Commands:
 
-        run                     run default GoldRush pipeline: GoldRush-Path + Polisher (GoldRush-Edit by default) + Tigmint-long + ntLink (
+        run                     run default GoldRush pipeline: GoldRush-Path + Polisher (GoldPolish by default) + Tigmint-long + ntLink (
 default 5 rounds)
         goldrush-path           run GoldRush-Path
-        path-polish             run GoldRush-Path, then GoldRush-Edit
-        path-tigmint            run GoldRush-Path, then GoldRush-Edit, then Tigmint-long
-        path-tigmint-ntLink     run GoldRush-Path, then GoldRush-Edit, then Tigmint-long, then ntLink (default 5 rounds)
+        path-polish             run GoldRush-Path, then GoldPolish
+        path-tigmint            run GoldRush-Path, then GoldPolish, then Tigmint-long
+        path-tigmint-ntLink     run GoldRush-Path, then GoldPolish, then Tigmint-long, then ntLink (default 5 rounds)
 
         General options (required):
         reads                   read name [reads]. File must have .fq or .fastq extension, but do not include the suffix in the supplied read name
@@ -80,7 +80,7 @@ default 5 rounds)
         w_ntLink                window size for minimizers [250]
         rounds                  number of rounds of ntLink [5]
 
-        GoldRush-Edit options:
+        GoldPolish options:
         polisher_mapper         Whether to use ntlink or minimap2 for mappings [minimap2]
         shared_mem		Shared memory path where polishing occurs [/dev/shm]
 
@@ -140,7 +140,7 @@ GoldRush has been tested on *Linux* operating systems (centOS7, ubuntu-20.04)
  * [boost](https://www.boost.org/doc/libs/1_61_0/more/getting_started/unix-variants.html)
  * [libdivsufsort](https://github.com/y-256/libdivsufsort)
  * [sparsehash](https://github.com/sparsehash/sparsehash)
- * [btllib](https://github.com/bcgsc/btllib)
+ * [btllib 1.6.2+](https://github.com/bcgsc/btllib)
  * [Tigmint 1.2.6+](https://github.com/bcgsc/tigmint)
  * [ntLink 1.3.3+](https://github.com/bcgsc/ntlink)
  * [minimap2](https://github.com/lh3/minimap2)
@@ -183,7 +183,7 @@ Compiling GoldRush from the source code takes ~2.5min on a typical machine.
  ```
 Running the above `goldrush_test_demo.sh` script will automatically download a small set of long reads from a ~1Mbp segment of *C. elegans* chromosome 3, and run GoldRush. It will also check that the final assembly file has an L50 of 1, as expected (ie. at least half of the assembly is in a single piece). The test should run in <2min on a typical machine.
 
-The final assembly file for the test demo can be found in: `goldrush_test_golden_path.goldrush-edit-polished.span2.dist500.tigmint.fa.k40.w250.ntLink-5rounds.fa`
+The final assembly file for the test demo can be found in: `goldrush_test_golden_path.goldpolish-polished.span2.dist500.tigmint.fa.k40.w250.ntLink-5rounds.fa`
 
 ## Citation
 If you use GoldRush in your research, please cite:

bin/goldrush

@@ -6,12 +6,12 @@
 # Input files
 reads=reads
 
-polisher=goldrush-edit
+polisher=goldpolish
 polished_infix=$(polisher)-polished
 # ntlink or minimap2
 polisher_mapper=minimap2
 
-# Shared memory location for GoldRush-Edit
+# Shared memory location for GoldPolish
 shared_mem=/dev/shm
 
 # ntlink mapping parameter (used if polisher_mapper=ntlink)
@@ -21,16 +21,16 @@ polish_w=100
 # Set max number of user processes
 set_ulimit=goldrush-ulimit
 
-ifeq ($(polisher), goldrush-edit)
-polisher_logs=GoldRush-Edit
+ifeq ($(polisher), goldpolish)
+polisher_logs=GoldPolish
 else
 polisher_logs=$(polisher)
 endif
 
 ifeq ($(polisher_mapper),ntlink)
-goldrush_edit_opts=--ntlink --k-ntlink $(polish_k) --w-ntlink $(polish_w)
+goldpolish_opts=--ntlink --k-ntlink $(polish_k) --w-ntlink $(polish_w)
 else ifeq ($(polisher_mapper),minimap2)
-goldrush_edit_opts=--minimap2
+goldpolish_opts=--minimap2
 else
 $(error "Unknown mapper: $(polisher_mapper)")
 endif
@@ -117,7 +117,7 @@ time=command memusg -t -o $@.time
 endif
 endif
 
-.PHONY: help run version clean path-tigmint-ntlink path-polish goldrush-path racon goldrush-edit path-tigmint tigmint ntLink-with-tigmint check-G check-reads
+.PHONY: help run version clean path-tigmint-ntlink path-polish goldrush-path racon goldpolish path-tigmint tigmint ntLink-with-tigmint check-G check-reads
 .DELETE_ON_ERROR:
 .SECONDARY:
 
@@ -136,7 +136,7 @@ help:
 	@echo ""
 	@echo "	Commands:"
 	@echo ""
-	@echo "	run			run default GoldRush pipeline: GoldRush-Path + Polisher (GoldRush-Edit by default) + Tigmint-long + ntLink (default 5 rounds)"
+	@echo "	run			run default GoldRush pipeline: GoldRush-Path + Polisher (GoldPolish by default) + Tigmint-long + ntLink (default 5 rounds)"
 	@echo ""
 	@echo "	goldrush-path		run GoldRush-Path"
 	@echo "	path-polish		run GoldRush-Path, then $(polisher_logs)"
@@ -179,7 +179,7 @@ help:
 	@echo "	w_ntLink		window size for minimizers [$(w_ntLink)]"
 	@echo "	rounds			number of rounds of ntLink [$(rounds)]"
 	@echo ""
-	@echo "	GoldRush-Edit options:"
+	@echo "	GoldPolish options:"
 	@echo "	polisher_mapper		Whether to use ntlink or minimap2 for mappings [$(polisher_mapper)]"
 	@echo "	shared_mem		Shared memory path where polishing occurs [/dev/shm] "
 	@echo ""
@@ -229,14 +229,14 @@ $(p1)_$(M).fq: $(long_reads)
 	$(time) racon -u -t$(t) $(long_reads) $^ > $@
 	echo "Done GoldRush-Path + $(polisher_logs)! $(polisher_logs) polished golden path can be found in: $@"
 
-%.goldrush-edit-polished.fa: %.fa $(long_reads)
-	$(time) $(set_ulimit) goldrush-edit $(goldrush_edit_opts) -t$(t) -m$(shared_mem) $< $(long_reads) $@
+%.goldpolish-polished.fa: %.fa $(long_reads)
+	$(time) $(set_ulimit) goldpolish $(goldpolish_opts) -t$(t) -m$(shared_mem) $< $(long_reads) $@
 	echo "Done GoldRush-Path + $(polisher_logs)! $(polisher_logs) polished golden path can be found in: $@"
 
 # Run racon
 racon: $(p2).racon-polished.fa check-G check-reads
 
-goldrush-edit: $(p2).goldrush-edit-polished.fa check-G check-reads
+goldpolish: $(p2).goldpolish-polished.fa check-G check-reads
 
 $(p2).fa.$(long_reads).sam: $(p2).fa $(long_reads)
 	$(time) minimap2 -t $(t) -a -x map-ont  $< $(long_reads) > $@

meson.build

@@ -15,7 +15,7 @@ btllib_dep = compiler.find_library('btllib')
 
 subdir('goldrush_path')
 subdir('bin')
-subproject('goldrush-edit')
+subproject('goldpolish')
 
 rootpath = meson.source_root()
 

requirements.txt

@@ -5,7 +5,7 @@ sdsl-lite
 boost-cpp
 libdivsufsort
 sparsehash
-btllib <=1.4.10
+btllib >=1.6.2
 python
 minimap2
 tigmint

subprojects/goldpolish

@@ -9,9 +9,9 @@ curl -L --output test_reads.fq https://www.bcgsc.ca/downloads/btl/goldrush/test/
 echo "Launching GoldRush"
 goldrush run reads=test_reads G=1e6 t=4 p=goldrush_test -B
 
-l50=$(abyss-fac goldrush_test_golden_path.goldrush-edit-polished.span2.dist500.tigmint.fa.k40.w250.ntLink-5rounds.fa |awk '{print $3}' |tail -n1)
+l50=$(abyss-fac goldrush_test_golden_path.goldpolish-polished.span2.dist500.tigmint.fa.k40.w250.ntLink-5rounds.fa |awk '{print $3}' |tail -n1)
 
-if [ -e goldrush_test_golden_path.goldrush-edit-polished.span2.dist500.tigmint.fa.k40.w250.ntLink-5rounds.fa ] && [ ${l50} -eq 1 ]; then
+if [ -e goldrush_test_golden_path.goldpolish-polished.span2.dist500.tigmint.fa.k40.w250.ntLink-5rounds.fa ] && [ ${l50} -eq 1 ]; then
   echo -e "\nTest successful!"
 else
   echo -e "\nTest failed - please check your installation"