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docs/From10X/README.md

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+---
+sort: 2
+---
+
+# Data from 10X Genomics
+## 快速上手指南
+本文档集合用于记录10X Genomics的WDL工具的操作说明。不负责对具体参数的完全解释。
+对于参数的解释，请参考[10X Genomics官方文档](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/algorithms)。
+
+文档集合的结构如下所示
+{% include list.liquid all=true %}

docs/From10X/scRNA-seq/README.md

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+# scRNA-seq
+您的位置：source: `{{ page.path }}`
+
+# 10X Genomics scRNA-seq
+为了便于工作流的可重复性，我们推荐您使用json文件来描述和存档您的实验参数。
+
+# 写在前面
+这里会涉及到BioOS文件管理的相关内容，请参考[BioOS文件管理（待完善）](../BioOS/README.md)
+
+在这里，我们假设您已经对平台的使用有了基础的了解，并创建了必要的文件夹。如果还没有，请参考[动手学BioOS计算](../BioOS/README.md)
+
+请注意，我们不要求您对json文件、WDL文件或者云计算有深入的了解，您只需要知道如何使用json文件来描述您的实验参数。我们的目标是您只需要知道如何“复制、粘贴”就能完成您的实验。
+
+让我们开始吧！
+
+## 对于一个典型的10X Genomics scRNA-seq实验，我们推荐使用如下的json文件：
+```json
+{
+  "cellranger_count_workflow.chemistry": "auto",
+  "cellranger_count_workflow.cpu": 32,
+  "cellranger_count_workflow.disk_space": "300 GB",
+  "cellranger_count_workflow.fastq_file_paths": null,
+  "cellranger_count_workflow.memory": "225 GB",
+  "cellranger_count_workflow.no_bam": "False",
+  "cellranger_count_workflow.reference_genome_tar_gz": "s3://bioos-wcnjupodeig44rr6t02v0/Example_10X_data/RAW/refdata-cellranger-GRCh38-3.0.0.tar.gz",
+  "cellranger_count_workflow.run_id": null,
+  "cellranger_count_workflow.sample": null,
+  "cellranger_count_workflow.secondary": "False"
+}
+```
+
+
+# 示例代码块
+
+以下是一个带行号的 JSON 代码块示例：
+
+<pre class="line-numbers"><code class="language-json">
+{
+  "cellranger_count_workflow": {
+    "chemistry": "auto",
+    "cpu": 32,
+    "disk_space": "300 GB",
+    "fastq_file_paths": [
+      "s3://bioos-wcnjupodeig44rr6t02v0/Example_10X_data/ERR8048237/5891STDY8062334_S1_L001_I1_001.fastq.gz",
+      "s3://bioos-wcnjupodeig44rr6t02v0/Example_10X_data/ERR8048237/5891STDY8062334_S1_L001_R1_001.fastq.gz",
+      "s3://bioos-wcnjupodeig44rr6t02v0/Example_10X_data/ERR8048237/5891STDY8062334_S1_L001_R2_001.fastq.gz"
+    ],
+    "memory": "225 GB",
+    "no_bam": "False",
+    "reference_genome_tar_gz": "s3://bioos-wcnjupodeig44rr6t02v0/Example_10X_data/RAW/refdata-cellranger-GRCh38-3.0.0.tar.gz",
+    "run_id": "ERR8048237",
+    "sample": "5891STDY8062334",
+    "secondary": "False"
+  }
+}
+</code></pre>
+
+请参考上面的 JSON 配置示例。
+
+看起来很复杂，但没关系。仔细观察，您会发现，这个json文件的部分参数已经自动设置好了，在大部分情况下，您只需要依次填写您自己的参数即可。
+
+（markdown格式 引用 可折叠 或者 展开上标引用）注释：作为快速上手教程，我们不对具体的参数做出解释，具体的参数的解释请参考[10X Genomics官方文档](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count)，在支持文档，我们也会对一些关键参数做出解释。
+
+这里我们给出了填写示例：
+- 注意这几个部分1️⃣`cellranger_count_workflow.fastq_file_paths` 2️⃣`cellranger_count_workflow.run_id` 3️⃣`cellranger_count_workflow.sample`
+
+```json
+{
+  "cellranger_count_workflow.chemistry": "auto",
+  "cellranger_count_workflow.cpu": 32,
+  "cellranger_count_workflow.disk_space": "300 GB",
+  "cellranger_count_workflow.fastq_file_paths": [
+    "s3://bioos-wcnjupodeig44rr6t02v0/Example_10X_data/ERR8048237/5891STDY8062334_S1_L001_I1_001.fastq.gz",
+    "s3://bioos-wcnjupodeig44rr6t02v0/Example_10X_data/ERR8048237/5891STDY8062334_S1_L001_R1_001.fastq.gz",
+    "s3://bioos-wcnjupodeig44rr6t02v0/Example_10X_data/ERR8048237/5891STDY8062334_S1_L001_R2_001.fastq.gz"
+  ],
+  "cellranger_count_workflow.memory": "225 GB",
+  "cellranger_count_workflow.no_bam": "False",
+  "cellranger_count_workflow.reference_genome_tar_gz": "s3://bioos-wcnjupodeig44rr6t02v0/Example_10X_data/RAW/refdata-cellranger-GRCh38-3.0.0.tar.gz",
+  "cellranger_count_workflow.run_id": "ERR8048237",
+  "cellranger_count_workflow.sample": "5891STDY8062334",
+  "cellranger_count_workflow.secondary": "False"
+}
+```
+
+是的，就是这么简单。我们添加了文件路径，并填写了run_id和sample。这和您在本地计算的参数填写逻辑是一样的。我们已经准备好了，现在就提交任务吧！
+
+## 提交任务
+让我们回到BioOS平台，来到我们的cellrangerTest页面。试试看，找到页面上的"运行参数"选项卡>输入参数>"上传JSON文件"，将您的json文件上传。
+
+然后，点击页面上的绿色按钮"开始分析"，等待任务完成。
+
+<figure style="
+  text-align: center;
+  display: inline-block;
+  border: 2px solid #00326e; /* 边框颜色，可根据需要调整 */
+  border-radius: 10px; /* 圆角半径 */
+  padding: 10px; /* 内边距，确保内容不紧贴边框 */
+  background-color: #f9f9f9; /* 背景颜色，可选 */
+">
+  <img src="../../Pics/scRNA-seq_fig.1.png" alt="注意右上角的绿色按钮，点击即可开始分析，并在3秒后自动跳转到分析历史界面。" style="width:auto; height:auto;"/>
+  <figcaption style="
+    font-size: 0.9em; /* 字体大小，稍小于正文 */
+    font-weight: bold; /* 加粗 */
+    text-decoration: underline; /* 下划线 */
+    color: inherit; /* 颜色与父元素一致 */
+    margin-top: 8px; /* 图片与注释之间的间距 */
+  ">
+    注意右上角的绿色按钮，点击即可开始分析，并在3秒后自动跳转到分析历史界面。
+  </figcaption>
+</figure>
+
+
+
+## 查看结果
+任务完成后，您可以在分析历史中看到您的任务。点击任务名称，进入任务详情页面。在任务详情页面，您可以查看/下载结果。
+
+<figure style="
+  text-align: center;
+  display: inline-block;
+  border: 2px solid #00326e; /* 边框颜色，可根据需要调整 */
+  border-radius: 10px; /* 圆角半径 */
+  padding: 10px; /* 内边距，确保内容不紧贴边框 */
+  background-color: #f9f9f9; /* 背景颜色，可选 */
+">
+  <img src="../../Pics/scRNA-seq_fig.2.png" alt="现在这张图片展示了任务分析历史的详情，你可以在这里再次查阅输入和输出参数。当然你也可以在这里查看或下载结果。" style="width:auto; height:auto;"/>
+  <figcaption style="
+    font-size: 0.9em; /* 字体大小，稍小于正文 */
+    font-weight: bold; /* 加粗 */
+    text-decoration: underline; /* 下划线 */
+    color: inherit; /* 颜色与父元素一致 */
+    margin-top: 8px; /* 图片与注释之间的间距 */
+  ">
+    现在这张图片展示了任务分析历史的详情，你可以在这里再次查阅输入和输出参数。当然你也可以在这里查看或下载结果。
+  </figcaption>
+</figure>
+
+点击"查看"，让我们来看看结果吧！所有的结果文件都会列出在这里，除了结果之外，也包括运行日志等文件，这取决于WDL文件的具体设置。
+
+<figure style="
+  text-align: center;
+  display: inline-block;
+  border: 2px solid #00326e; /* 边框颜色，可根据需要调整 */
+  border-radius: 10px; /* 圆角半径 */
+  padding: 10px; /* 内边距，确保内容不紧贴边框 */
+  background-color: #f9f9f9; /* 背景颜色，可选 */
+">
+  <img src="../../Pics/scRNA-seq_fig.3.png" alt="所有的结果文件都会列出在这里。" style="width:auto; height:auto;"/>
+  <figcaption style="
+    font-size: 0.9em; /* 字体大小，稍小于正文 */
+    font-weight: bold; /* 加粗 */
+    text-decoration: underline; /* 下划线 */
+    color: inherit; /* 颜色与父元素一致 */
+    margin-top: 8px; /* 图片与注释之间的间距 */
+  ">
+    现在这张图片展示了所有的结果文件。
+  </figcaption>
+</figure>
+
+在这个示例中，我们需要的文件在"outs"文件夹中，让我们逐渐深入文件夹，找到我们需要的文件。
+
+<figure style="
+  text-align: center;
+  display: inline-block;
+  border: 2px solid #00326e; /* 边框颜色，可根据需要调整 */
+  border-radius: 10px; /* 圆角半径 */
+  padding: 10px; /* 内边距，确保内容不紧贴边框 */
+  background-color: #f9f9f9; /* 背景颜色，可选 */
+">
+  <img src="../../Pics/scRNA-seq_fig.4.png" alt="我们逐级打开目录，到最后一层。" style="width:auto; height:auto;"/>
+  <figcaption style="
+    font-size: 0.9em; /* 字体大小，稍小于正文 */
+    font-weight: bold; /* 加粗 */
+    text-decoration: underline; /* 下划线 */
+    color: inherit; /* 颜色与父元素一致 */
+    margin-top: 8px; /* 图片与注释之间的间距 */
+  ">
+    让我们逐级打开目录，到最后一层。具体的层次设置和WDL文件的设置有关。
+  </figcaption>
+</figure>
+
+比如，我们希望直接拿到filtered_feature_bc_matrix.h5ad文件，点击"下载"，我们可以下载结果。
+
+<figure style="
+  text-align: center;
+  display: inline-block;
+  border: 2px solid #00326e; /* 边框颜色，可根据需要调整 */
+  border-radius: 10px; /* 圆角半径 */
+  padding: 10px; /* 内边距，确保内容不紧贴边框 */
+  background-color: #f9f9f9; /* 背景颜色，可选 */
+">
+  <img src="../../Pics/scRNA-seq_fig.5.png" alt="现在，在你点击下载之后，你可以直接在浏览器的下载工具栏看到下载进度。" style="width:auto; height:auto;"/>
+  <figcaption style="
+    font-size: 0.9em; /* 字体大小，稍小于正文 */
+    font-weight: bold; /* 加粗 */
+    text-decoration: underline; /* 下划线 */
+    color: inherit; /* 颜色与父元素一致 */
+    margin-top: 8px; /* 图片与注释之间的间距 */
+  ">
+    你只需要点击下载按钮，便可以直接通过浏览器进行数据下载。
+  </figcaption>
+</figure>
+
+🎊Bravo!🎊 到此为止，您已经掌握了BioOS的基本使用方法，并成功完成了一次10X Genomics scRNA-seq的分析。👏👏👏
+
+# 如果我有很多数据呢？
+
+**🤔好，那么好，这时候可能就会有人问了，如果我们有很多数据，也要像这样一个一个点击吗？**
+
+    非常好的问题！当你尝试把一件简单的事情重复做上一万遍的时候，其复杂度将会指数增加。
+
+**当然不是**，我们在这里只展示了BioOS的冰山一角，BioOS的真正能力将在您尝试构建数据模型/实体之后展现。下面，让我们从一个稍微复杂的例子开始，一步一步的学习如何调度BioOS强大的计算能力。
+
+

docs/README.md

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+---
+sort: 1
+---
+
+# Quick_Start_in_BioOs
+
+
+# SRA_Analysis_WDL
+- An Auto Pipeline
+- Robustness
+- Designed for Bio-os
+
+Here, we need a script, a program or an other things, to meet our need. 
+
+[![Typing SVG](https://readme-typing-svg.herokuapp.com?font=Courier+New&pause=1000&color=6B4DF7&multiline=true&random=false&width=435&height=80&lines=%E7%AB%99++%E5%9C%A8++%E5%B7%A8++%E4%BA%BA++%E7%9A%84++%E8%82%A9++%E8%86%80++;Stand+on+the+shoulders+of+giants)](https://git.io/typing-svg)
+
+What we need?
+-----------------------
+We have a platform built for fetch raw sequencing data to our system. Once the data is under our gover, we will get our pipline on woring. Given the complexity of the situation, our tools should be packaged as stand-alone toolkits, or they should take advantage of infrastructure that is readily available.
+
+
+What we have,now
+-----------------------
+  - 10X Cellranger count WDL
+  - 10X Cellranger ATAC count WDL
+  - 10X Cellranger VDJ WDL
+  - 10X Spaceranger WDL
+  - 10X Cellranger multi WDL (for GEX + VDJ-T/VDJ-B or both of them)
+  - SeqWell & Drop-seq & BD WDL (STARsolo)
+  - SMART-seq WDL (STARsolo, too)
+`Praise the god of STAR`
+
+  - Dockers at here: `https://hub.docker.com/repositories/ooaahhdocker`
+
+
+Update
+-----------------------
+
+### 2024.10.10 : let's have a try
+Try using rust as an encapsulation for the command part of the wdl, replacing python.
+The results are here: `_SRAtoFastqgz/2.0_rust`. 
+
+I'm looking forward to this being a start, a start to be able to judge the type of vdj files (or any other files) quickly.
+
+### 2024.10.9 : ATTENTON!
+All of those images' name should be replaced as followed.
+  - **registry-vpc.miracle.ac.cn/gznl/**
+    - registry-vpc.miracle.ac.cn/gznl/ooaahhdocker/ooaahhdocker/python_pigz:1.0
+    - registry-vpc.miracle.ac.cn/gznl/ooaahhdocker/py39_scanpy1-10-1
+    - registry-vpc.miracle.ac.cn/gznl/ooaahhdocker/starsolo2:3.0
+    - registry-vpc.miracle.ac.cn/gznl/ooaahhdocker/starsolo2:2.0
+    - registry-vpc.miracle.ac.cn/gznl/python:3.9.19-slim-bullseye
+
+### 2024.5.14 : Function added
+  - For cellranger count WDL, updated naming conventions of h5ad files.
+    - `filtered_feature_bc_matrix.h5ad` convert to `~{sample}_filtered_feature_bc_matrix.h5ad`
+
+### 2024.5.11 : Refining Code Logic
+  - When handling the extraction of SRA files to fastq files, an issue with file attribution was encountered, making it difficult to accurately determine the correct naming of the extracted fastq files. Solution: The R1 data contains a large number of duplicate sequences composed of barcodes and UMIs. When performing high compression ratio file compression, the size of the R1 data file should be smaller than that of R2.
+  - Simply reverse the order of the file compression and renaming logic.
+
+### 2024.5.9 : multi need to set NA as []
+  - Array[File] Cannot accept input with an empty string, use [] as insted.
+
+
+### 2024.5.4 : Updated naming logic for files
+  - The extent of the impact "SRA > fastq.gz"
+
+### 2024.4.28 : Added unplanned WDL files
+  - 10X Cellranger multi WDL
+
+### 2024.4.28 : Bugs fix
+  - For VDJ files(SRA), we have to use parameters: "`--split-file` combined with `--include-technologies`".
+  - ps. For SpaceRanger, we need to use parameters `--split-3`. Therefore, in the case of 10X, we need to choose the appropriate workflow for the specific situation.
+
+### 2024.4.26 : Function added
+  - For local fastq files, I had added `cellranger_singleFile.wdl`.
+
+### 2024.4.23 : Function added
+  - Increased the output of h5ad&bam files as much as possible.
+
+### 2024.4.22 : Added STARsolo WDL files, which could used in BD&SeqWell&Dropseq, without umitools.
+  - ps. Set `--soloBarcodeReadLength=0` to skip the barcode and umi checks.
+  - Docker pull: ooaahhdocker/starsolo2:3.0, with python3.9/scanpy1.10.1/star2.7.11 inside.
+  - Attention!
+    - To make the agreement between STARsolo and CellRanger even more perfect, you can add
+
+    `args_dict['--genomeSAsparseD'] = ['3']`
+
+    - CellRanger 3.0.0 use advanced filtering based on the EmptyDrop algorithm developed by Lun et al. This algorithm calls extra cells compared to the knee filtering, allowing for       cells that have relatively fewer UMIs but are transcriptionally different from the ambient RNA. In STARsolo, this filtering can be activated by:
+
+    `args_dict['--soloCellFilter'] =['EmptyDrops_CR']`
+
+### 2024.4.16 : Must come with full image information, slide number, etc.
+  - For spaceranger, complete image information is a must, and the data provided by some authors is incomplete.
+
+### 2024.4.12 : The technical roadmap has been updated, and sra files are now reused using fasterq-dump
+  - Docker pull: ooaahhdocker/python_pigz:1.0 with python3.9/pigz, which meet fastq file to fastq compressed file fast implementation.
+
+### 2024.4.11 : Resolving compatibility issues
+  - Lower versions of cellranger(2.9.6) are unable to handle newer 10X scRNA-seq data.
+  - Added a way to externally import the cellranger package
+
+## 音频
+<audio controls>
+  <source src="music/Retirement.mp3" type="audio/mp3">
+</audio>
+
+## 视频youtobe width="560" height="315" style="position: relative; padding-bottom: 56.25%; height: 0; overflow: hidde
+<div style="position: relative; padding-bottom: 56.25%; height: 0; overflow: hidden;">
+  <iframe width="560" height="315" src="https://www.youtube.com/embed/mgbjhzDndOY?si=n7WVtwtU2q5XKxft" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+</div>
+
+## 视频bilibili position: relative; padding-bottom: 56.25%; height: 0; overflow: hidden allowfullscreen=true
+<div style="position: relative; padding-bottom: 56.25%; height: 0; overflow: hidden;">
+  <iframe src="//player.bilibili.com/player.html?isOutside=true&aid=113350260297623&bvid=BV1QvyHYeEuE&cid=26410156129&p=1" scrolling="no" border="0" frameborder="no" framespacing="0" allowfullscreen="true"></iframe>
+</div>
+
+
+## 视频bilibili2 style="position: relative; padding: 30% 45% style="position: absolute; width: 100%; height: 100%; left: 0; top: 0;" rameborder="no" scrolling="no
+
+<div style="position: relative; padding: 30% 45%;">
+
+<iframe style="position: absolute; width: 100%; height: 100%; left: 0; top: 0;" src="https://player.bilibili.com/player.html?aid=76053337&;bvid=BV11J41127DF&cid=130096191&page=1&as_wide=1&high_quality=1&danmaku=0" frameborder="no" scrolling="no">
+
+</iframe>
+
+</div>

docs/music/README.md

@@ -0,0 +1 @@
+test