diff --git a/README.md b/README.md index 1e8ea4dc80780bb7d1352495c0108bacca6bccfa..690fbe93e1641a520ea02d2be74fe1ba80ec9983 100644 --- a/README.md +++ b/README.md @@ -5,9 +5,9 @@ ## Description -This repository contains the software **BioFlow-Insight** written in Python. **BioFlow-Insight** automatically analyses the code of Nextflow workflows and extracts useful information, particularly in the form of visual graphs depicting the workflow's structure and representing its different steps. +This repository contains **BioFlow-Insight**, a Python software tool. **BioFlow-Insight** automatically analyses Nextflow workflow code, extracting useful information, notably in the form of visual graphs illustrating the workflow's structure and its various steps. -**BioFlow-Insight** is easily installable as a Python package (see here). It is also accesible as a web service (see [here](https://bioflow-insight.pasteur.cloud/)). +**BioFlow-Insight** is easily installable as a Python package (see here). It is also accessible as a web service (see [here](https://bioflow-insight.pasteur.cloud/)). <!--The outputs of **BioFlow-Insight** are saved in the results folder.--> @@ -28,7 +28,7 @@ This repository contains the software **BioFlow-Insight** written in Python. **B ### Using from source -The python packages needed are described in the `requirements.txt` file. +BioFlow-Insight's dependencies are given in the `requirements.txt` file. > Note : To install graphviz, in linux you might need to execute this command `sudo apt install graphviz` @@ -57,7 +57,7 @@ The 3 different graphs generated by **BioFlow-Insight** are : 2. The second graph represents operations without any inputs, along with processes and their dependencies. This graph, called the *dependency graph without branch operations*, is obtained by removing the branch operations and linking the remaining elements if a path exists between them in the original specification graph. 3. The final graph, called the *process dependency graph*, represents only processes and their dependencies. Similar to the latter, this graph is constructed by removing all operations, leaving only processes, and linking them based on their dependencies in the original specification graph. -> To examplify **BioFlow-Insight** utilisation, let's use the rnaseq-nf workflow proposed by Nextflow (its source code can be found [here](https://github.com/nextflow-io/rnaseq-nf/tree/8253a586cc5a9679d37544ac54f72167cced324b)). +> To examplify **BioFlow-Insight** utilisation, let's use the rnaseq-nf workflow proposed by Nextflow (its source code can be found [here](https://github.com/nextflow-io/rnaseq-nf/tree/8253a586cc5a9679d37544ac54f72167cced324b)). Examples of the output are given below. ### Input @@ -87,7 +87,7 @@ w.generate_all_graphs(render_graphs = True, processes_2_remove=[]) ### Output -After the workflow has been analysed and the graphs genrated, the outputs are saved in the `results` folder. +After the workflow has been analysed and the graphs generated, the outputs are saved in the `results` folder. The structure of this folder is organised as such : @@ -134,8 +134,8 @@ The structure of this folder is organised as such : └── ro-crate-metadata-rnaseq-nf.json ``` -* The `ro-crate-metadata-rnaseq-nf.json` describes the workflow following an extended Workflow [RO-Crate](https://www.researchobject.org/ro-crate/) profile which can be found [here]() (TODO). -* the `debug` folder contains different intermediary files which are ussefull for debugging +* The `ro-crate-metadata-rnaseq-nf.json` describes the workflow following an extended Workflow [RO-Crate](https://www.researchobject.org/ro-crate/) profile. The description of this extended profile can be found [here]() (TODO) +* the `debug` folder contains different intermediary files which are ussefull for debugging * the `graphs` folder contains the different graphs which are generated. For each of the 3 graphs described above, **BioFlow-Insight** generates : * A `json` file which describes the graph using **BioFlow-Insight** specific format * A `json` file which describes the metadata which are extracted from the graph @@ -143,6 +143,12 @@ The structure of this folder is organised as such : > For each graph **BioFlow-Insight** generates it in the `mermaid` format and the dot `dot` format. If the `render_graphs` option is set to `True`, the `png` image is also generated. +These are the graphs which are generated by **BioFlow-Insight**, they are rendered using Graphviz (png). + +| <img align="center" src="img/specification_graph.png" > | <img align="center" src="img/dependency_graph_wo_branch_operations.png"> | <img align="center" src="img/process_dependency_graph.png" > | +|:-:|:-:|---| +| Specification Graph | Dependency Graph without branch operations | Process Dependency Graph | + ## License diff --git a/img/dependency_graph_wo_branch_operations.png b/img/dependency_graph_wo_branch_operations.png new file mode 100644 index 0000000000000000000000000000000000000000..2808d2d4103ac2770fb9abe09883b1011b1f0769 Binary files /dev/null and b/img/dependency_graph_wo_branch_operations.png differ diff --git a/img/process_dependency_graph.png b/img/process_dependency_graph.png new file mode 100644 index 0000000000000000000000000000000000000000..147ef338ded82c9b1d632cc1df1e446e56f78ce2 Binary files /dev/null and b/img/process_dependency_graph.png differ diff --git a/img/specification_graph.png b/img/specification_graph.png new file mode 100644 index 0000000000000000000000000000000000000000..8f6102dd64c468c936b0ec2901b8007d80526163 Binary files /dev/null and b/img/specification_graph.png differ