updated readme

README.md

 # About
 
-Comparing genome and gene reconstruction when using short reads (Illumina), long reads (Oxford Nanopore Technology, ONT)
-and a hybrid approach.
+Comparing genome and gene reconstruction when using short reads (SR) (Illumina) only, long reads (LR) (Oxford Nanopore Technology) only and a hybrid approach (Hy).
 
 # Setup
 
@@ -9,35 +8,112 @@ and a hybrid approach.
 git clone --recurse-submodules https://git-r3lab.uni.lu/susheel.busi/ont_pilot_gitlab
 ```
 
-[About git submodules](https://git-scm.com/book/en/v2/Git-Tools-Submodules)
+## Conda
 
-TODO: other dependencies ???
+[Conda user guide](https://docs.conda.io/projects/conda/en/latest/user-guide/index.html)
 
-# Analysis
-
-## On LCSB HPC server `iris`
-
-Main `conda` environment: `/scratch/users/vgalata/miniconda3/ONT_pilot`
+```bash
+# install miniconda3
+wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+chmod u+x Miniconda3-latest-Linux-x86_64.sh
+./Miniconda3-latest-Linux-x86_64.sh # follow the instructions
+```
 
-Example commands for `GDB`:
+Create the main `snakemake` environment
 
 ```bash
-# conda
-conda activate /scratch/users/vgalata/miniconda3/ONT_pilot
-# analysis: check which rules will be executed
-snakemake -s workflow/Snakefile --configfile config/GDB/config.yaml --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline --cores 1 -rpn
-# submit jobs using slurm
-./config/GDB/sbatch.sh
-# report
-snakemake -s workflow_report/Snakefile --configfile config/GDB/config.yaml --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline --cores 1 -rpn
+# create venv
+conda env create -f requirements.yml -n "YourEnvName"
 ```
 
-### `conda` environment
+## Configs
 
-If the path specified above does not exists, you can create the environment from `requirements.yaml`
-and replace the env. path in `sbatch.sh` files by `"ONT_pilot"`.
+All config files are stored in the folder `config/`: sub-folders contain files for all the samples and/or pipeline steps.
 
-```bash
-# will create env. ONT_pilot
-conda env create -f requirements.yaml
-```
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+- samples: `gdb`, `nwc`, `rumen`, `zymo`
+- pipeline steps: `rawdata`
+
+*TODO: remove aquifer and gcall*
+
+The sub-folders contain:
+- config YAML file(s) (`config(.substep)?.yaml`) for a `Snakemake` workflow
+- `slurm` config YAML file(s) (`slurm(.substep)?.yaml`) defining job submission parameters for a `Snakemake` workflow
+- bash script(s) to execute a `Snakemake` workflow (`sbatch(.substep)?.sh`)
+
+# Workflows
+
+1. Download public datasets (*TODO: what about GDB?*)
+2. Run the FAST5 workflow (per sample)
+3. Run the main analysis workflow (per sample)
+4. Create reports (per sample)
+5. Create figures for the paper
+
+Relevant paremters which have to be changed are listed for each workflow and config file.
+Parameters defining system-relevant settings are not listed but should be also be changed if required, e.g. number of threads used by certain tools etc.
+
+## Raw data workflow
+
+Download raw data required for the analysis.
+
+*TODO: remove aquifer*
+
+- config: `config/rawdata/`
+  - `config.yaml`:
+    - change `work_dir`
+  - `sbatch.sh`
+    - change `SMK_ENV`
+    - if not using `slurm` to submit jobs remove `--cluster-config`, `--cluster` from the `snakemake` CMD
+  - `slurm.yaml` (only relevant if using `slurm` for job submission)
+- workflow: `workflow_rawdata/`
+
+## FAST5 workflow
+
+Process raw FAST5 files of a sample
+- create a multi-FAST5 file from single-FAST5 files
+- do basecalling
+
+This step is **not** required if the long-read FASTQ file is already available.
+
+- config:
+  - per sample
+  - `config/<sample>/config.fast5.yaml`
+    - change `work_dir`, `single_fast5_dir`, `multi_fast5_dir`, `basecalling_dir`
+    - change `guppy:gpu:path` and `gyppy:gpu:bin`
+  - `config/<sample>/sbatch.fast5.yaml`
+    - change `SMK_ENV`
+    - if not using `slurm` to submit jobs remove `--cluster-config`, `--cluster` from the `snakemake` CMD
+  - `config/<sample>/slurm.fast5.yaml` (only relevant if using `slurm` for job submission)
+- workflow: `workflow_fast5/`
+
+## Main workflow
+
+Main analysis workflow: given SR and LR FASTQ files, run all the steps to generate required output.
+This includes:
+- read preprocessing
+- assembly and assembly polishing
+- gene calling and annotation
+- additional analysis of the assemblies and their genes/proteins
+
+The workflow is run per sample and might require a couple of days to run depending on the sample and used configuration.
+
+- config:
+  - per sample
+  - `config/<sample>/config.yaml`
+    - change all path parameters
+  - `config/<sample>/sbatch.yaml`
+    - change `SMK_ENV`
+    - if not using `slurm` to submit jobs remove `--cluster-config`, `--cluster` from the `snakemake` CMD
+  - `config/<sample>/slurm.yaml` (only relevant if using `slurm` for job submission)
+- workflow: `workflow/`
+
+*TODO: remove unsed parameters, e.g. canu, gtdbtk etc.*
+
+## Report workflow
+
+This workflow creates plots and an HTML report for a sample using the output of the main workflow.
+
+*TODO*
+
+## Creating figures for the paper
+
+*TODO*
\ No newline at end of file