AHdeRojas/16s-qiime2

Analysis of microbiome samples in CWL using QIIME2

16S Multipart Workflows

• Step1: Import Demux: 16s-step1-import-demux-paired.cwl
• Step2: DADA2: 16s-step2-dada2-paired.cwl
• Step3: Alpha analysis: 16s-step3-alpha-beta-analysis

Based upon https://docs.qiime2.org/2018.4/tutorials/moving-pictures/

Details

Step1

• Obtaining and importing data
• Demultiplexing sequences

Visualize 16s-step1-import-demux-paired.cwl at view.commonwl.org

Step2

Before running this step a user must determine dada2_trunc_len_f, dada2_trunc_len_r and dada2_trim_left_f, dada2_trim_left_r parameters. This can be done based on plots you see in demux.qzv created in Step1.

• DADA2
• FeatureTable and FeatureData summaries
• Generate a tree for phylogenetic diversity analyses
• Taxonomic analysis
• Differential abundance testing with ANCOM

Visualize 16s-step2-dada2-paired.cwl at view.commonwl.org

Step3

Before running this step a user must determine diversity_sampling_depth and rarefaction_max_depth parameters. diversity_sampling_depth can be determined by looking at table.qzv from Step2. rarefaction_max_depth can be determined by looking at table.qzv (Frequency per sample).

• Alpha and beta diversity analysis
• Alpha rarefaction plotting

Visualize 16s-step3-alpha-beta-analysis.cwl at view.commonwl.org

Summary

Each sub-step above corresponds to a cwl sub-workflow in the subworkflows/ directory with the qiime2 prefix. Each command within these sub-workflows corresponds to a CWL CommandLineTool in tools/qime2/ directory.

Visualize workflows and subworkflows at view.commonwl.org.