New branch so that goldpolish submodule is up-to-date

azure-pipelines.yml

@@ -15,7 +15,7 @@ jobs:
   - script: |
       source activate goldrush_CI
       conda install --yes -c conda-forge mamba python=3.10 
-      mamba install --yes -c conda-forge -c bioconda compilers meson gperftools sdsl-lite boost-cpp sparsehash btllib libdivsufsort minimap2 tigmint ntlink miller  
+      mamba install --yes -c conda-forge -c bioconda compilers meson gperftools sdsl-lite boost-cpp sparsehash btllib libdivsufsort minimap2 tigmint ntlink miller snakemake intervaltree  
     displayName: Install dependencies
   - script: |
       source activate goldrush_CI
@@ -48,7 +48,7 @@ jobs:
   - script: |
       source activate goldrush_CI
       conda install --yes -c conda-forge mamba python=3.10
-      mamba install --yes -c conda-forge -c bioconda compilers meson gperftools sdsl-lite boost-cpp sparsehash btllib libdivsufsort minimap2 tigmint ntlink miller 
+      mamba install --yes -c conda-forge -c bioconda compilers meson gperftools sdsl-lite boost-cpp sparsehash btllib libdivsufsort minimap2 tigmint ntlink miller snakemake intervaltree 
     displayName: Install dependencies
   - script: |
       source activate goldrush_CI

bin/goldrush

@@ -308,5 +308,5 @@ ntLink_softlink: $(p2).$(polished_infix).span$(span).dist$(dist).tigmint.fa.k$(k
 # Run GoldPolish-Target after ntLink rounds
 goldpolish_target: $(p2).$(polished_infix).span$(span).dist$(dist).tigmint.fa.k$(k_ntLink).w$(w_ntLink).ntLink-$(rounds)rounds.polished.fa check-G check-reads
 %.k$(k_ntLink).w$(w_ntLink).ntLink-$(rounds)rounds.polished.fa: %.k$(k_ntLink).w$(w_ntLink).ntLink-$(rounds)rounds.fa
-	$(time) goldpolish --target --k-ntlink $(target_k_ntlink) --w-ntlink $(target_w_ntlink) -l $(target_flank_length) $< $(long_reads) $(p2).$(polished_infix).span$(span).dist$(dist).tigmint.fa.k$(k_ntLink).w$(w_ntLink).ntLink-$(rounds)rounds
+	$(time) goldpolish --target --k-ntlink $(target_k_ntlink) --w-ntlink $(target_w_ntlink) -l $(target_flank_length) $< $@
 	echo "Done GoldRush-Path + $(polisher_logs) + Tigmint-long + $(rounds) ntLink rounds + GoldPolish-Target! Your final assembly can be found in: $@"

tests/goldrush_test_demo.sh

@@ -11,7 +11,7 @@ goldrush run reads=test_reads G=1e6 t=4 p=goldrush_test  -B
 
 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.goldpolish-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.polished.fa ] && [ ${l50} -eq 1 ]; then
   echo -e "\nTest successful!"
 else
   echo -e "\nTest failed - please check your installation"