From af412da081ed9e796127eef91d9dff45a237ea13 Mon Sep 17 00:00:00 2001
From: coolneng <akasroua@gmail.com>
Date: Sat, 13 Nov 2021 17:59:32 +0100
Subject: [PATCH] Update README

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 README.org | 59 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 59 insertions(+)

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+* Adapter parser
+
+This tool parses fastqc reports to extract the adapter sequences, from the *Overrepresented sequences*, and then outputs them to a text file.
+
+** Technologies
+
+- Pandas
+
+** Installation
+
+This project uses [[https://nixos.org][Nix]] to ensure reproducible
+builds.
+
+1.  Install Nix (compatible with MacOS, Linux and
+    [[https://docs.microsoft.com/en-us/windows/wsl/about][WSL]]):
+
+#+begin_src bash
+curl -L https://nixos.org/nix/install | sh
+#+end_src
+
+2.  Clone the repository:
+
+#+begin_src bash
+git clone https://git.coolneng.duckdns.org/coolneng/adapter-parser
+#+end_src
+
+3.  Change the working directory to the project:
+
+#+begin_src bash
+cd adapter-parser
+#+end_src
+
+4.  Enter the nix-shell:
+
+#+begin_src bash
+nix-shell
+#+end_src
+
+After running these commands, you will find yourself in a shell that
+contains all the needed dependencies.
+
+** Usage
+
+The program expects a folder containing the fastqc reports as an input and an output file where to store the sequences in the FASTA format.
+
+#+begin_src bash
+python src/parser.py <input> <output>
+#+end_src
+
+#+RESULTS:
+:
+: usage: parser.py [-h] input output
+:
+: positional arguments:
+:   input       directory containing the fastqc reports
+:   output      file where to export the sequences
+:
+: optional arguments:
+:   -h, --help  show this help message and exit