wget https://github.com/nf-core/ampliseq/raw/master/environment.yml #创建流程所需要的环境 conda env create-n ampliseq--file environment.yml #激活环境 conda activate ampliseq #安装nextflow conda install-c bioconda nextflow-y 二、配置和运行 配置主要是参考github上这个流程的参数说明[1],主要是控制...
nfcore/ampliseqis a bioinformatics analysis pipeline used for amplicon sequencing, supporting denoising of any amplicon and supports a variety of taxonomic databases for taxonomic assignment including 16S, ITS, CO1 and 18S. Phylogenetic placement is also possible. Multiple region analysis such as 5R ...
Amplicon sequencing analysis workflow using DADA2 and QIIME2 - nf-core linting · Workflow runs · nf-core/ampliseq
wget https://github.com/nf-core/ampliseq/raw/master/environment.yml #创建流程所需要的环境 conda env create -n ampliseq --file environment.yml #激活环境 conda activate ampliseq #安装nextflow conda install -c bioconda nextflow -y 二、配置和运行 配置主要是参考github上这个流程的参数说明,主要是控...
Hi, I tried to run the nextflow pipeline for a small dataset but encountered an error. The commands I used: nextflow run nf-core/rrna-ampliseq \ -profile standard,docker \ -name "test1" \ -r 1.0.0 \ --reads '/home/nutrition_group/desktop...
input = "https://raw.githubusercontent.com/nf-core/test-datasets/ampliseq/samplesheets/Samplesheet.tsv" // Custom reference taxonomy qiime_ref_tax_custom = "https://raw.githubusercontent.com/MatthewJM96/test-datasets/ampliseq/testdata/db/85_greengenes.fna.gz,https://raw.githubusercontent.com...
// // This file holds several functions specific to the main.nf workflow in the nf-core/ampliseq pipeline // import nextflow.Nextflow class WorkflowMain { // // Citation string for pipeline // public static String citation(workflow) { return "If you use ${workflow.manifest.name} ...
If necessary, also make a PR on the nf-core/ampliseqbranchon thenf-core/test-datasetsrepository. Make sure your code lints (nf-core lint). Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[nf-core/ampliseq] Pipeline Complete ERROR ~ Error executing process > 'dada_single (172,137)' Caused by: Processdada_single (172,137)terminated with an error exit status (1) Command executed: IFS=',' read -r -a trunclen <<< "172,137" ...
If necessary, also make a PR on the nf-core/ampliseq branch on the nf-core/test-datasets repository. Make sure your code lints (nf-core pipelines lint). Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>). Check for unexpected warnings in debug mode...