Merge pull request #15 from bcgsc/remove_ntedit_submodule

Remove ntEdit submodule

Author: warrenlr

.gitmodules

@@ -1,3 +0,0 @@
-[submodule "subprojects/ntEdit"]
-	path = subprojects/ntEdit
-	url = https://github.com/bcgsc/ntEdit.git

README.md

@@ -37,24 +37,16 @@ conda install -c bioconda -c conda-forge ntroot
 
 Installing ntRoot from the source code:
 ```
-git clone --recurse-submodules https://github.com/bcgsc/ntRoot.git
+git clone https://github.com/bcgsc/ntRoot.git
 cd ntRoot
-meson setup build --prefix=/path/to/install/directory
-cd build
-ninja install
 ```
-ntRoot and all required scripts will be installed to: /path/to/install/directory
+No compilation is required for ntRoot (only the dependencies), so simply add the ntRoot repository to your PATH.
 
 ### Dependencies <a name=dependencies></a>
 - python 3.9+
 - perl
-- [meson](https://mesonbuild.com/)
-- [ninja](https://ninja-build.org/)
+- [ntEdit 2.0.1+](https://github.com/bcgsc/ntEdit)
 - [snakemake](https://snakemake.readthedocs.io/en/stable/)
-- [btllib](https://github.com/bcgsc/btllib)
-- [boost](https://www.boost.org/doc/libs/1_61_0/more/getting_started/unix-variants.html)
-- [ntCard](https://github.com/bcgsc/ntCard)
-- [ntHits](https://github.com/bcgsc/ntHits)
 - [samtools](https://www.htslib.org/)
 
 

azure-pipelines.yml

@@ -19,19 +19,12 @@ jobs:
   - script: |
       source activate ntroot_CI
       conda install --yes --name ntroot_CI -c conda-forge -c bioconda python=3.9 mamba
-      mamba install --yes -c conda-forge -c bioconda meson ninja snakemake perl btllib compilers boost-cpp ntcard nthits
+      mamba install --yes -c conda-forge -c bioconda meson ninja snakemake perl 'ntedit>=2.0.1' samtools
     displayName: Install Conda packages
   
   - script: |
       source activate ntroot_CI
-      meson setup build --prefix=$(pwd)/test_build
-      cd build
-      ninja install
-    displayName: Compile ntRoot
-  
-  - script: |
-      source activate ntroot_CI
-      export PATH=$(pwd)/test_build/bin:$PATH
+      export PATH=$(pwd):$PATH
       which ntroot
       cd demo
       ./run_ntroot_demo.sh
@@ -55,19 +48,12 @@ jobs:
   - script: |
       source activate ntroot_CI
       conda install --yes --name ntroot_CI -c conda-forge -c bioconda python=3.9 mamba
-      mamba install --yes -c conda-forge -c bioconda meson ninja snakemake perl btllib compilers boost-cpp ntcard nthits
+      mamba install --yes -c conda-forge -c bioconda snakemake perl 'ntedit>=2.0.1' samtools
     displayName: Install Conda packages
   
   - script: |
       source activate ntroot_CI
-      meson setup build --prefix=$(pwd)/test_build
-      cd build
-      ninja install
-    displayName: Compile ntRoot
-  
-  - script: |
-      source activate ntroot_CI
-      export PATH=$(pwd)/test_build/bin:$PATH
+      export PATH=$(pwd):$PATH
       which ntroot
       cd demo
       ./run_ntroot_demo.sh

bin/meson.build

@@ -64,7 +64,7 @@ rule ntedit_reads:
         params = f"-k {k} -t {t} -z {z} -j {j} -Y {Y} --solid ",
         vcf_input = f"-l {l}" if l else ""
     shell:
-        "{params.benchmark} run-ntedit snv --draft {reference} --reads {reads_prefix} {params.params} "
+        "{params.benchmark} run-ntedit snv --reference {reference} --reads {reads_prefix} {params.params} "
         "{params.vcf_input}"
 
 rule ntedit_genome:
@@ -81,7 +81,7 @@ rule ntedit_genome:
         params = f"-k {k} -t {t} -z {z} -j {j} -Y {Y}",
         vcf_input = f"-l {l}" if l else ""
     shell:
-        "{params.benchmark} run-ntedit snv --draft {reference} --genome {input.genomes} {params.params} "
+        "{params.benchmark} run-ntedit snv --reference {reference} --genome {input.genomes} {params.params} "
         " {params.vcf_input}"
 
 rule samtools_faidx: