update README

README.md

@@ -2,7 +2,7 @@
 
 ![GitHub last commit (branch)](https://img.shields.io/github/last-commit/yonesora56/plant2human/main)
 ![Status](https://img.shields.io/badge/status-development-yellow)
-[![cwltool](https://img.shields.io/badge/cwltool-3.1.20241112140730-success)](https://github.com/common-workflow-language/cwltool/releases/tag/3.1.20241112140730)
+[![cwltool](https://img.shields.io/badge/cwltool-3.1.20250110105449-success)](https://github.com/common-workflow-language/cwltool/releases/tag/3.1.20250110105449)
 [![License](https://img.shields.io/badge/License-MIT-blue.svg)](./LICENSE)
 [![Version](https://img.shields.io/badge/version-1.0.1-brightgreen)](https://github.com/yonesora56/plant2human/releases/tag/v1.0.1)
 [![Open in Dev Containers](https://img.shields.io/static/v1?label=Dev%20Containers&message=python3.11&color=blue&logo=docker)](https://github.com/yonesora56/plant2human/tree/main/.devcontainer)
@@ -14,6 +14,14 @@ Based on the list of genes you are interested in, you can easily create a scatte
 
  
 
+ 
+
+## report
+
+- 2025-02-02: fix foldseek easy-search process
+
+ 
+
 ## Implementation Background
 
 In recent years, with the [AlphaFold protein structure database](https://alphafold.ebi.ac.uk/), it has become easier to obtain protein structure prediction data and perform structural similarity searches even for plant species such as rice. Against this background, searching for hits with **“low sequence similarity and high structural similarity”** for the gene groups being focused on has become possible. This approach may allow us to discover proteins that are conserved in distantly related species and to consider the characteristics of these proteins based on the wealth of knowledge we have about humans.
@@ -24,14 +32,21 @@ In recent years, with the [AlphaFold protein structure database](https://alphafo
 
 ### **1. Using Dev Containers (Docker and VScode extension)**
 
-You can create an analysis environment using [Dev Containers](./.devcontainer/devcontainer.json), a VScode extension.
-Please check the official website for details.
+Most processes, such as Foldseek, use container (BioContainers), but some involve processing with jupyter notebook, which requires the preparation of some python libraries (e.g., polars.).
+If you want to experiment with a simple workflow, you can create an analysis environment easily using [Dev Containers](./.devcontainer/devcontainer.json) system, a VScode extension.
+Using this environment, the version of the python library is probably the one used during development, so errors are unlikely to occur (see [Dockerfile](./.devcontainer/Dockerfile) for the package version).
+
+Please check the official website for Dev Container details.
 - [Developing inside a Container](https://code.visualstudio.com/docs/devcontainers/containers)
 - [Development Containers](https://containers.dev/)
 
+ 
+
 ### **2. Executing with cwltool**
 
-This analysis workflow is tested using [cwltool](https://github.com/common-workflow-language/cwltool) version 3.1.20241112140730.
+This analysis workflow is tested using [cwltool](https://github.com/common-workflow-language/cwltool) version 3.1.20250110105449.
+
+ 
 
  
 
@@ -80,9 +95,11 @@ The execution results are output with the [jupyter notebook](./test/oryza_sativa
 
  
 
+ 
+
 ### **2. Creating and Preparing Indexes**
 
-I'm sorry, but the [main workflow](./Workflow/plant2human_v1.0.1.cwl) does not currently include the creation of an index (both for foldseek index and BLAST index).
+I'm sorry, but the [main workflow](./Workflow/plant2human_v1.0.1.cwl) does not currently include the creation of an index process (both for foldseek index and BLAST index).
 Please perform the following processes in advance.
 
 #### 2-1. Creating a Foldseek Index
@@ -94,14 +111,14 @@ Please select the database you want to use from `Alphafold/UniProt,` `Alphafold/
 You can check the details of this database using the following command.
 
 ```bash
-docker run --rm quay.io/biocontainers/foldseek:9.427df8a--pl5321hb365157_1 foldseek databases --help
+docker run --rm quay.io/biocontainers/foldseek:9.427df8a--pl5321h5021889_2 foldseek databases --help
 ```
 
 For example, if you want to specify AlphaFold/Swiss-Prot as the index, you can do so with the following command,
 
 ```bash
 # using docker container
-docker run -u $(id -u):$(id -g) --rm -v $(pwd):/home -e HOME=/home --workdir /home quay.io/biocontainers/foldseek:9.427df8a--pl5321hb365157_1 foldseek databases Alphafold/Swiss-Prot swissprot tmp --threads 8
+docker run -u $(id -u):$(id -g) --rm -v $(pwd):/home -e HOME=/home --workdir /home quay.io/biocontainers/foldseek:9.427df8a--pl5321h5021889_2 foldseek databases Alphafold/Swiss-Prot swissprot tmp --threads 8
 
 # making directory
 mkdir ./index/index_swissprot
@@ -132,7 +149,7 @@ gzip -d uniprotkb_9606_all.fasta.gz
 
  
 
-### 3. Execution of the [Main Workflow](./Workflow/plant2human_v1.0.1.cwl)
+### 3. Execution of the [Main Workflow](./Workflow/plant2human.cwl)
 
 In this process, we perform a structural similarity search using the `foldseek easy-search` command and then perform a pairwise alignment of the amino acid sequences of the hit pairs using the `needle` and `water` commands.
 Finally, based on this information, we create a scatter plot and output a [jupyter notebook](./test/oryza_sativa_test/plant2human_report.ipynb) as a report.
@@ -155,8 +172,4 @@ The following scatter diagram can also be obtained from the test results of [Zey
 
 ![image](./image/zey_mays_scatter_plot.png)
 
- 
-
-## Citation
-
-[![DOI](https://img.shields.io/badge/DOI-10.48546%2FWORKFLOWHUB.WORKFLOW.1206.3-blue)](https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.1206.3)
+