Beta

“Polishing the Diamond”

Release note: “2024-05-13” (YYYY-MM-DD)

According to the initial plan, all workflows have been developed. After two weeks of continuous testing, all expected functionalities have been realized. Additionally, the unplanned development of cellranger multi has been completed, and h5ad file output has been added. It is important to note that for non-10X workflows, special attention should be paid to the fact that their results may not be directly comparable to those of cellranger.

To address this issue, I have predefined some parameters for STARsolo. For details, please refer to the STARsolo manual at 'https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md'. Additionally, STARsolo theoretically supports any droplet-based or even non-droplet-based single-cell RNA sequencing data, and it also works for bulk RNA sequencing. The current STARsolo workflow can be run directly without umitools, as long as you have a whitelist file and a clear index sequence structure. The current STARsolo workflow does not include direct support for 10X sequencing data because I have adjusted some parameters specifically for seq-well and drop-seq, and these adjustments are not exposed to users. If users have similar requirements, they will need to make their own adjustments. Overall, after years of development, STAR's flexibility has exceeded my previous expectations. In the future, STAR may accompany us on a longer journey.

开发记录

Anyway，暂时停一下，开发过程困难重重，但是好在没有耽误研发计划。#动手学WDL#，这次借助GPTs在什么也不了解的情况下从0开发WDL，一边看报错一边学语法规则。阅读WDL的报错信息有些困难，info级别的信息和真正的报错信息混杂在一起，就像是一位絮絮叨叨的老奶奶👵。这次也学着搭配了docker，对k8s也有了一定了解。
观自在，「觀自在」是觀世音菩薩的另外一個名號，意思是說，只要你能觀照自己，你能認識自己，你就可以自在了！这次我即是开发者又是用户，游走在不同背景的一线用户和开发者、甲方之间，得益于这一点，我能够不断的转换我观察的角色。每次和各方沟通完回来，我都在想，用户为什么又这样，开发者为什么又那样。前几天我在准备些复盘记录了，脑子里就突然闪过上次和另一个组的沟通过程，我就对自己说，啊，原来是这样。没有什么“又这样”或者“又那样”，事情本来就是这样的，人类就是这样的，事物的发展就是这样的规律，有其自在，我却是着相了。你看佛经，佛经的文字是固定的，但是解读却很多，每个人从固定的经文里看到自己。你看西方哲学，很多从亚里士多德到海德格尔、黑格尔，大家都在说我真理啊被说出来了的时候就不存在了，在尝试证明存在的存在本身，想要bing。道非道，非常道，能讲出来的道理就不是道理了，从佛祖拈花到伽叶一笑的飞跃，需要读者自己来完成了。所以更需要观自在了，这点倒是很像昨天看的肖尔算法，认识到世间的规律并化为己用啊，很神奇，算法学家们就像做这样的事情，真神奇。或者说科学的基本范式就是发现规律并利用规律，要说起利用规律，着就又是自由的一个范畴了，所以孔夫子要讲从心所欲不逾矩，心所欲是规律本身，自然不逾矩了。

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

Full Changelog: https://github.com/OOAAHH/SRA_Analysis_WDL/commits/Beta