From f7c198aed32d7412de99dc942d40c840e4eb02c7 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Fri, 8 Mar 2024 14:17:17 +0100
Subject: [PATCH] update readme
---
README.md | 28 ++++++----------------------
1 file changed, 6 insertions(+), 22 deletions(-)
diff --git a/README.md b/README.md
index 6928a5f..fff86fb 100644
--- a/README.md
+++ b/README.md
@@ -68,29 +68,13 @@ The 3 different graphs generated by **BioFlow-Insight** are :
### Input
-In this example, we are going to use the **BioFlow-Insight** source code. After cloning both repositories (this one and the rnaseq-nf workflow). We can run the following command to run the analyses (the different steps are described below) :
-
-```python
-import os
-current_path= os.getcwd()
-os.chdir("bioflow-insight/")
-from src.workflow import Workflow
-os.chdir(current_path)
-
-w = Workflow("./rnaseq-nf/main.nf", duplicate=False, display_info=True)
-w.initialise()
-w.generate_all_graphs(render_graphs = True, processes_2_remove=[])
-```
+In this example, we are going to use the **BioFlow-Insight** tool to analyse the rna-seq workflow. After installing **BioFlow-Insight** via pip, and cloning the the rnaseq-nf repository. Simply run this command line :
+
+
-1. line 1 to 5 : import the `Workflow` object allowing the analysis
-2. line 6 : create the object `w` corresponding to `Workflow`
- 1. line 6 : the first parameter is the address of the main Nextflow file (obligatory paramter).
- 2. line 6 : parameter `duplicate` (by default `False`), in the case some processes and subworkflows are duplicated in the workflow by the `include as` option, this parameter will duplicate the elements in the graphs.
- 3. line 6 : parameter `display_info` (by default `True`), shows the files which are being analysed
-3. line 7 : `initialise` runs the entire analysis of the Nextflow workflow
-4. line 8 : `generate_all_graphs` generates all the graphs in the mermaid and dot formats + the associated metadata for the graphs
- 1. line 8 : parameter `render_graphs` (by default `True`), if true the png images of the dot graphs are generated thanks to Graphviz. For large workflows this can sometimes fail (depending on the hardware).
- 2. line 8 : parameter `processes_2_remove` (by default `[]`), is a list of processes which are to be removed from the graphs. This is usefull in the cas of `MULTIQC` processes (they don't really serve a functionnal role but can cluter the structure since they are connected to the majority of processes).
+```
+bioflow-insight rnaseq-nf/main.nf
+```
### Output
--
GitLab