# nextflow 安装, 需要java 11curl -s https://get.nextflow.io|bash# 测试exportNXF_VER=23.10.1 nextflow run hello-world# nf-core 安装, 我使用的是python3.8,nf-core版本为2.14.1pip install nf-core 安装流程 下载对应的rnaseq流程 # 下载流程git clone https://github.com/nf-core/rnaseq.git 下...
nextflow run nf-core/rnaseq \ --input samplesheet.csv \ --genome GRCh37 \ -profile <docker/singularity/podman/conda/institute> 真正可运行的脚本,需要设置以下多种参数 # 首先我们切换到输出目录 cd /public/home/rnaseq # 这个 alias 命令很重要,因为官方的 pipeline 里找不到 hisat2_extract_splice...
source /home/conda/miniconda3/bin/activate env_nf nextflow run nf-core/rnaseq \ --input /path/to/samplesheet.csv \ --outdir /path/to/output/ \ --genome GRCh37 \ --aligner 'star_salmon' \ -profile singularity \ --max_memory '64.GB' \ --max_cpus 16 \ --max_time '240.h' \...
nf-core/rnafusion was written by Martin Proks (@matq007), Maxime Garcia (@maxulysse) and Annick Renevey (@rannick) We thank the following people for their help in the development of this pipeline: Phil Ewels Rickard Hammarén Alexander Peltzer ...
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 6 7 8 9 10 11 12 nextflow run nf-core-rnaseq-3.6/workflow/\# 格式就是nextflow run <下载好的nf-core-rnaseq文件夹下workflow文件夹的目录> ...
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: # You can use this file to create a conda environment for this pipeline: # conda env create -f environment.yml ...
问Nextflow真的不一致还是我使用nf/rnaseq做错了什么？EN最近看到生信技能树的一篇推文在介绍nf-core这个...
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...
nf-rnaSeqMetagen was also extended to work with other metagenomics studies using RNA-seq data and adapted to work on different computational platforms. The nf-rnaSeqMetagen pipeline is freely available on GitHub (https://github.com/phelelani/nf-rnaSeqMetagen)....
To address these shortcomings, we present nf-core/circrna, a workflow for the quan- tification, miRNA target prediction and differential expression analysis of circRNAs in RNA-Seq data developed using nextflow [28]. The pipeline has been developed under the specifications of the nf-core framework...