fix: added missing dag.

Author: rabioinf

README.md

@@ -26,7 +26,6 @@ If you use this workflow in a paper, don't forget to give credits to the authors
 
 _Workflow overview:_
 
-<!-- include overview-->
 <img src="resources/images/dag.svg" align="center" />
 
 ## Workflow overview
@@ -72,14 +71,14 @@ conda activate snakemake-assembly-postprocessing
 To run the workflow from command line, change the working directory.
 
 ```bash
-cd path/to/snakemake-simple-mapping
+cd snakemake-assembly-postprocessing
 ```
 
 Adjust options in the default config file `config/config.yml`.
 Before running the complete workflow, you can perform a dry run using:
 
 ```bash
-snakemake --dry-run
+snakemake --cores 1 --dry-run
 ```
 
 To run the workflow with test files using **conda**:

config/README.md

@@ -10,34 +10,6 @@ A Snakemake workflow for the post-processing of microbial genome assemblies.
 3. Create a QC report for the assemblies using [Quast](https://github.com/ablab/quast)
 4. Create a pangenome analysis (orthologs/homologs) using [Panaroo](https://gthlab.au/panaroo/)
 
-## Installation
-
-**Step 1: Clone this repository**
-
-```bash
-git clone https://github.com/MPUSP/snakemake-assembly-postprocessing.git
-cd snakemake-assembly-postprocessing
-```
-
-**Step 2: Install dependencies**
-
-It is recommended to install snakemake and run the workflow with `conda` or `mamba`. [Miniforge](https://conda-forge.org/download/) is the preferred conda-forge installer and includes `conda`, `mamba` and their dependencies.
-
-**Step 3: Create snakemake environment**
-
-This step creates a new conda environment called `snakemake-assembly-postprocessing`.
-
-```bash
-mamba create -c conda-forge -c bioconda -n snakemake-assembly-postprocessing snakemake pandas
-conda activate snakemake-assembly-postprocessing
-```
-
-**Step 4: Install PGAP**
-
-- if you want to use [PGAP](https://github.com/ncbi/pgap) for annotation, it needs to be installed separately
-- PGAP can be downloaded from https://github.com/ncbi/pgap. Please follow the installation instructions there.
-- Define the path to the `pgap.py` script (located in the `scripts` folder) in the `config` file (recommended: `./resources`)
-
 ## Running the workflow
 
 ### Input data
@@ -48,3 +20,5 @@ The samplesheet table has the following layout:
 | sample | species                  | strain | id_prefix | file           |
 | ------ | ------------------------ | ------ | --------- | -------------- |
 | EC2224 | "Streptococcus pyogenes" | SF370  | SPY       | assembly.fasta |
+
+**Note:** Pangenome analysis with `Panaroo` requires at least two samples.