add readme for configuration

config/README.md

@@ -0,0 +1,34 @@
+# Usage and configuration
+
+Here is a rough overview:
+1. Install [conda](https://docs.conda.io/en/latest/miniconda.html) (mamba or miniconda is fine).
+2. Install snakemake with:
+```bash
+conda install -c conda-forge -c bioconda snakemake
+```
+3. Download checkm2 database (via `wget https://zenodo.org/api/files/fd3bc532-cd84-4907-b078-2e05a1e46803/checkm2_database.tar.gz`)
+4. Download GTDB-Tk database (via `wget https://data.gtdb.ecogenomic.org/releases/release220/220.0/auxillary_files/gtdbtk_package/full_package/gtdbtk_r220_data.tar.gz`)
+3. [Download the latest release from this repo](https://github.com/richardstoeckl/basecallNanopore/releases/latest) and cd into it
+4. Edit the `config/config.yaml` to provide the paths to your results/logs directories, and the paths to the databases you downloaded, as well as any parameters you might want to change.
+5. Edit the `config/sampleData.csv` file with the specific details for each assembly you want to check. Depending on what you enter here, the pipeline will automatically adjust what will be done.
+
+---
+
+# General configuration
+
+To configure this workflow, modify `config/config.yaml` according to your needs, following the explanations provided in the file.
+
+## "Main" section
+
+Here you should provide the paths to your intermediary/results/logs directories. The `interim` directory will contain larger intermediary files. The `results` directory will contain the final output of the pipeline. The `log`directory will be used to store the log files for each step.
+Here you should also write the name of your sample data file (see [relevant section below](#sampleData-file-setup)).
+
+## "Tools" section
+
+Here you should give the paths to the databases needed for some of the tools.
+
+
+# sampleData file setup
+
+The setup of the samples is specified via comma-separated values files (`.csv`).
+You can use the `config/sampleData.csv`file as a template.

config/config.yaml

@@ -1,5 +1,5 @@
 main:
-    sampleData: "sampleData.csv" # "config/sampleData_tests.csv is the sample file that can be used for testing the pipeline setup"
+    sampleData: "sampleData.csv" # "config/sampleData.csv is the sample file that can be used for testing the pipeline setup"
     logPath: "logs/"
     interimPath: "interim/"
     resultPath: "results/"