exportNXF_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 -s singularity -x none -u amend --force 共42个镜像: 下载测试数据(gith...
槽点一:过度包装,徒增复杂性 我们就以其官网提供的核心流程 RNA-seq 为例,来看看这东西到底有多复杂。下面是流程目录。 代码语言:javascript 代码运行次数:0 运行 AI代码解释 rnaseq/├── assets ├── bin ├──CHANGELOG.md ├──CITATIONS.md ├──CODE_OF_CONDUCT.md ├── conf ├── docs ...
# 运行 nextflow sh nextflow-21.04.3-all run /nf-core-rnaseq-3.4/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> --input samplesheet.csv \ # 就是上一步我们用python脚本生成的samplesheet.csv文件 --fasta Homo_sapiens.GRCh38.dna.primary_assembly.fa \...
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> --input samplesheet.csv \# 就是上一步我们用python脚本生成...
之前文章介绍了Nextflow:《Nextflow-完整pipeline编写执行利器》,nf-core就是基于Nextflow开发的一个生物信息平台,包含如:scRNA-seq、RNA-seq、Hi-C、ATAC-seq、ChIP-seq等流程,每种流程都配有相应的文档和示例: 目前截止2020年11月,共有发布版本26个,开发中的流程15个,归档4个。基本上涵盖了当前生物信息数据分析...
我们将使用Nextflow来编写一个处理RNA-Seq数据的流程脚本。创建一个名为rna_seq.nf的文件,并在文件中添加以下代码: AI检测代码解析 #定义输入参数params.input = ""#定义流程process align { input: file fastq from params.inputoutput: file 'aligned.bam' into alignment_chscript: ...
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. ...
RNA-seq data from skin samples of patients with the systemic sclerosis (SSc) disease were used to test the pipeline and to identify possible pathogens, so as to better understand the onset and progression of the disease. A number of bacterial species belonging to Arthrobacter, Bacillus, ...
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control. workflowrna-seqpipelinenextflowrnanf-core UpdatedMar 26, 2025 Nextflow nextflow-io/awesome-nextflow Star585 Code Issues ...
我这里使用 Nextflow 作为流程搭建工具，它有着很多强大的功能：最近在做GEO数据挖掘的文章复现，文章标题...