nextflow run nf-core/ampliseq--reads"Dong-16S"\--FW_primerTACGGRAGGCAGCAG\--RV_primerAGGGTATCTAATCCT\--metadata"sample-metadata.txt"\--untilQ2import \--extension"/*R{1,2}.fastq"\--trunclenf280\--trunclenr250\--max_memory'3.GB'\--max_cpus2\--onlyDenoising 然后,就得到了输出结果:...
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...
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>).
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...
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...
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...
Breadcrumbs ampliseq /lib / WorkflowMain.groovyTop File metadata and controls Code Blame executable file· 77 lines (66 loc) · 3.1 KB Raw // // This file holds several functions specific to the main.nf workflow in the nf-core/ampliseq pipeline // import nextflow.Nextflow class ...
./nextflow run nf-core/ampliseq -profile standard,docker --reads '/mnt/hgfs/data/16srna20190531/' -c test.config -resume N E X T F L O W ~ version 19.04.1 Launching nf-core/ampliseq` [sick_feynman] - revision: f0357d6 [master] ,--./,-. _...