Pipelines " nf-core 目前涵盖了68个pipeline,包括RNA-seq, ATAC-seq,DNA-seq等,安装好环境可以直接用nextflow提交job进行分析。以atac分析流程为例 https://nf-co.re/atacseqInstall nextflow A DSL for pa…
离线下载nf-core/rnaseq nf-core download nf-core/rnaseq 加入--singularity,可以获取 Singularity container 什么是Singularity ?https://singularity.lbl.gov/ 下载下来会是一个安装包,解压即可 运行该流程,nextflow run <directory> https://nf-co.re/tools#downloading-pipelines-for-offline-use 使用iGenomes ...
Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! On release, automated continuous integration tests run the pipeline on a full-sized dataset on the ...
The nf-core framework for community-curated bioinformatics pipelines. Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. Nat Biotechnol.2020 Feb 13. doi:10.1038/s41587-020-0439-x. ...
bioinformatic pipelinespeak callingreproducible researchCrosslinking and immunoprecipitation (CLIP) technologies have become a central component of the molecular biologists' toolkit to study protein-RNA interactions and thus to uncover core principles of RNA biology. There has been a proliferation of CLIP-...
题目:The nf-core framework for community-curated bioinformatics pipelines 杂志:Nature Biotechnology 时间:Published: 13 February 2020 链接:https://www.nature.com/articles/s41587-020-0439-x 目前nf-core 共包含了27 种分析流程,如下: 而nf-core里面的不同流程,本质上就是一些测试数据和写好的配置文件,方...
每个nf-core 流程都会附带有docker,singularity和conda的配置文件。使用这些文件就可以指导流程运行相关软件。 共享配置 如果使用其他人共享的系统,最好去使用https:///nf-core/configs 的配置文件。这些是nf-core运行时所加载的配置。 您可能会发现您的系统已经有一个共享的配置文件(请参阅https://...
第一次使用一个流程,会调用nf-core/rnaseq/environment.yml 文件配置一个独立的conda环境(nf-core-rnaseq),安装一系列软件,如下: 代码语言:javascript 代码运行次数:0 运行 AI代码解释 # You can usethisfile to create a conda environmentforthispipeline:# conda env create-f environment.ymlname:nf-core-rn...
题目:The nf-core framework for community-curated bioinformatics pipelines 杂志:Nature Biotechnology 时间:Published: 13 February 2020 链接:https://www.nature.com/articles/s41587-020-0439-x 目前nf-core 共包含了27 种分析流程,如下: 而nf-core里面的不同流程,本质上就是一些测试数据和写好的配置文件,方...
Finding the Parabricks modules on nf-core Several Parabricks pipelines can be found on nf-core as modules. These modules can be dropped into existing workflows or used on their own. To read more about nf-core modules, see their documentation. To find the available Parabricks modules, visit ...