Automating qiime2 commands with bash script

[colinbrislawn (Colin J Brislawn)]

Hello Sam,

Yep, some have been built. These two use Snakemake:

Tourmaline: a workflow for rapid and reproducible amplicon sequence analysis using QIIME 2 and Snakemake

Announcing Tourmaline, a fully-featured Snakemake workflow for QIIME 2. Features include: Portability. Native support for Linux and macOS in addition to Docker containers. QIIME 2. The core commands of Tourmaline, including the DADA2 and Deblur packages, are all commands of QIIME 2, one of the most popular amplicon sequence analysis software tools available. You can print all of the QIIME 2 and other shell commands of your workflow before or while running the workflow. Snakemake. Managing the…

QIIME2 snakemake workflow tutorial - 18S/16S tag-sequencing

Tutorial: Run qiime2 for 18S or 16S tag-sequencing using snakemake Sarah Hu Summary: This tutorial was written with qiime2-2019.4 for 18S tag-sequencing (but can be adopted for any metabarcoding. Below tutorial uses an 18S dataset to go from raw fastq files to a complete ASV tutorial. I will continue to update this tutorial and add to it on the GitHub repos listed below. Tag-sequencing pipeline to generate ASVs - https://github.com/shu251/tagseq-qiime2-snakemake - input raw fastq sequences,…

You could also capture your common commands in a code notebook like Jupyter, then simply make a new copy of your notebook for each project, then modify and rerun as needed.