create V1.1

README.md

@@ -19,19 +19,24 @@ Assembly: https://www.ncbi.nlm.nih.gov/assembly/GCA_003402055.1
 
 ## Installation
 ```
-git clone --recursive https://forgemia.inra.fr/seqoccin/axis1-assembly.git
-cd axis1-assembly/GenomOrder
+git clone --recursive git@forgemia.inra.fr:seqoccin/GenomOrder.git
+cd GenomOrder
 ```
 
 ## Running the test pipeline
 To test the pipeline, first make sure that <a href="https://www.nextflow.io/docs/latest/getstarted.html"> Nextflow is installed with >v20.01.0 </a> <a href="https://docs.conda.io/projects/conda/en/latest/user-guide/install/"> and Conda is installed </a>
 
-Then:
+Then you can run it using conda:
+locally :
+```
+nextflow run main.nf -profile conda,local --reference data/GCA_003401745.fasta --assembly data/GCA_003402055.fasta --outdir ./TestPipeline/
+```
+Or on clusters (change, slurm to your cluster settings in conf/small.config):
 ```
 nextflow run main.nf -profile conda,small --reference data/GCA_003401745.fasta --assembly data/GCA_003402055.fasta --outdir ./TestPipeline/
 ```
 
-if you already have python3, minimap2 and samtools installed, you can just run :
+if you already have python3 (biopython package, os and argparse), minimap2 and samtools installed, you can just run :
 ```
 nextflow run main.nf -profile small --reference data/GCA_003401745.fasta --assembly data/GCA_003402055.fasta --outdir ./TestPipeline/
 ```