DualRNA-Seq分析流程

参考流程：https://nf-co.re/dualrnaseq/1.0.0/usage

Ewels P A, Peltzer A, Fillinger S, et al. The nf-core framework for community-curated bioinformatics pipelines[J]. Nature biotechnology, 2020, 38(3): 276-278.

• 软件安装

# Make sure that Java v8+ is installed:
java -version

# Install Nextflow
curl -fsSL get.nextflow.io | bash

# Add Nextflow binary to your user's PATH:
mv nextflow ~/bin/
# OR system-wide installation:
# sudo mv nextflow /usr/local/bin

• conda安装

conda create -n dualrnaseq
conda activate dualrnaseq
conda install nextflow

• 下载pipeline

nextflow run nf-core/dualrnaseq -profile test,<docker/singularity/conda/institute>

• 基本的运行方式

nextflow run nf-core/dualrnaseq/main.nf -profile docker \
--input "/folder_to_reads/*_R{1,2}.fq.gz" \
--fasta_host host.fa \
--fasta_pathogen pathogen.fa \
--gff_host host.gff \
--gff_pathogen pathogen.gff \
--run_star \
--outdir results

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