Merge branch 'main' into condatest

.misc/condadeps

@@ -0,0 +1,12 @@
+ bzip2=1.0.8=h7f98852_4
+ font-ttf-dejavu-sans-mono=2.37=hab24e00_0
+ pygraphviz=1.7=py39h78163bd_0
+ graphviz=2.47.1=h85b4f2f_1
+ imagemagick=7.0.11_13=pl5320hb118871_0
+ openjdk=8.0.312=h0d85af4_0
+ pandoc=2.13=h7f98852_0
+ python=3.9.4=hffdb5ce_0_cpython
+ r-base=4.0.5=h9e01966_1
+ r-tidyverse=1.3.1=r40hc72bb7e_0
+ sed=4.8=he412f7d_0
+ snakemake=6.4.0=hdfd78af_0

README.md

@@ -6,9 +6,7 @@ _It's Lep-Map3 and Lep-Anchor, but with snakes 🐍🐍_
 [![Cite](https://img.shields.io/badge/Cite-10.5281/zenodo.6055566-e1e1e1?style=for-the-badge)](https://zenodo.org/badge/latestdoi/260516189) 
 # LepWrap
 
-LepWrap is a reusable pipeline to use the linkage map software [Lep-Map3](https://sourceforge.net/projects/lep-map3/) and the genome assembly map-based anchoring and orienting software [Lep-Anchor](https://sourceforge.net/p/lep-anchor/wiki/Home/). It is the Snakemake-based successor to [LepMapp3r](https://github.com/pdimens/LepMapp3r). Check out [the wiki](https://github.com/pdimens/LepWrap/wiki) for detailed installation, usage, and workflow information.
-
-
+LepWrap is a reusable pipeline to use the linkage map software [Lep-Map3](https://sourceforge.net/projects/lep-map3/) and the genome assembly map-based anchoring and orienting software [Lep-Anchor](https://sourceforge.net/p/lep-anchor/wiki/Home/). Check out [the documentation/wiki](https://github.com/pdimens/LepWrap/wiki) for detailed installation, usage, and workflow information.
 
 ### How to install
 You will need a `conda` installation ([Anaconda](https://docs.anaconda.com/anaconda/install/) or [Miniconda](https://docs.conda.io/en/latest/miniconda.html), I recommend Miniconda). Alternatively, you can download latest release or clone this repository locally.
@@ -47,7 +45,7 @@ You will need to modify `config.yml` to suit your needs, then you can simply run
 ```bash
 LepWrap <number_of_cores> <config.yml>
 ```
-where `<number_of_cores>` is an integer of the maximum number of cores/threads you want the pipeline to use and `<config.yml>` (optional!) is the name of the config file, if it's different than `config.yml`. 
+where `<number_of_cores>` is an integer of the maximum number of cores/threads you want the pipeline to use and `<config.yml>` (optional!) is the name of the config file, if it's different than `config.yml`. If no config file is found in the directory, LepWrap will generate a default one for you to edit.
 
 **Examples**
 ```bash

rules/LepMap3/distances.smk

@@ -17,12 +17,10 @@ rule calculate_distances:
     threads: 2
     shell:
         """
-        cp {input.lg} {output.distance}
-        
+        cp {input.lg} {output.distance}       
         zcat {input.data_call} | java -cp $CONDA_PREFIX/bin/lepmap3 OrderMarkers2 evaluateOrder={input.lg} data=- {params.dist_method} numThreads={threads} improveOrder=0 sexAveraged=1 &> {output.sex_averagedtmp}
         sed -i -e 's/LG \= 0/LG \= {params.lg}/g' {output.sex_averagedtmp}
         sed -n '/\*\*\* LG \=/,$p' {output.sex_averagedtmp} > {output.sex_averaged} 
         awk '/#java/{{flag=1}} flag; /*** LG =/{{flag=0}}' {output.sex_averagedtmp} > {log.sex_averaged}
-
         zcat {input.data_call} | java -cp $CONDA_PREFIX/bin/lepmap3 OrderMarkers2 evaluateOrder={input.lg} data=- {params.dist_method} numThreads={threads} calculateIntervals={output.intervals} > {log.intervals} 2>&1
         """