nextflow测试rnaseq流程。 设置镜像下载目录,下载流程和singularity镜像: export NXF_SINGULARITY_CACHEDIR="singularity_db_pipe/rnaseq" # -s 下载流程时,选择下载singularity镜像 # -u 下载singularity镜像到$NXF_SINGULARITY_CACHEDIR目录中,不拷贝到流程目录中。 nf-core pipelines download rnaseq -r 3.18.0 -...
基于Nextflow的nf-core是生物信息学分析的集大成者 简单来说,它把各类组学分析中所有的流程整合在一起,我们只需要提供测序数据,就能完成复杂的上游分析。 但是在实际操作中,特别是在服务器的计算节点上跑nf-core时,还是会遇到各式各样的问题。这篇文章将带领从未接触过nextflow和nf-core的小白们,从0到1完成该些流...
1. 下载安装包: nextflow可以通过bioconda安装,所以这次我们只需要下载nf-core/rnaseq的安装包即可: 1 2 3 4 mamba create -n nextflow nextflow nf-core conda activate nextflow nf-core download nf-core/rnaseq tar-zxvf nf-core-rnaseq-3.4.tar.gz 此时我们可以通过nextflow运行这个安装包: 1 2 3 4 5...
问RNA-seq示例工作流中的nextflow .collect()方法ENcollect：收集器 Collector作为collect方法的参数 Collec...
StarScope 是达普生物自主开发的，其基于 STARsolo 和 Seurat 的 nextflow pipeline， 提供一站式的单细胞 RNA-seq 分析方案，可完成从原始的 reads 到细胞基因表达矩阵输出，并生成一个完整的 HTML 格式数据报告，表达结果还可接入多种下游分析。▉ 软件功能：3‘-RNA-seq pipeline • 通过 cutadapt 对原始 ...
If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data. Now, you can run the pipeline using: nextflow run jbrestel/bulkrnaseq \ -profile <docker/singularit...
RNASeq-NF execution relies onNextflowframework which provides an abstraction between the pipeline functional logic and the underlying processing system. This allows the execution of the pipeline in a single computer or in a HPC cluster without modifying it. ...
copying the main script and optionally the configuration file, which can then be modified for the individual use-case. The preferred installation method relies on Nextflow [27] to automatically pull pre-specified docker images at run-time unless they were previously downloaded; this approach is used...
The nf-rnaSeqMetagen pipeline presented in this study was developed using Nextflow as a workflow management system to orchestrate applications used in the pipeline and to handle input/output data between processes. All applications were containerized using Singularity to facilitate parallelization, ...
In the case of Nextflow and snakemake-based workflows, individual jobs are internally submitted for each pipeline component, and typically it is implicitly left to the user to worry about time specifica- tion for every component. To address this common use-case, we have written and tested ...