Workflow: QIIME2 Step 2 (DADA2 option)
Fetched 2023-01-10 19:49:12 GMT
Verified with cwltool version 3.1.20221201130942
QIIME2 DADA2, feature summaries, phylogenetic diversity tree, taxonomic analysis and ancom
- Selected
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| dada2_trim_left | Integer | ||
| dada2_trunc_len | Integer | ||
| sample_metadata | File | ||
| ancom_collapse_level | Integer | ||
| taxonomic_classifier | File | ||
| demux_sequences_artifact | File | ||
| ancom_filter_sample_query | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| dada2_sequences |
qiime2-step2-dada2.cwl#qiime2-03-dada2.cwl
(Workflow)
|
qiime2 DADA2 detect/correct sequence data |
Option 1: DADA2 from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/ |
| phylogenetic_tree | qiime2 create phylogenetic tree |
Generate a tree for phylogenetic diversity analyses from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/ |
|
| taxonomic_analysis | qiime2 explore sample taxonomic composition |
Taxonomic analysis from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/ |
|
| ancom_diff_abundance |
qiime2-step2-dada2.cwl#qiime2-09-ancom.cwl
(Workflow)
|
qiime2 identify differentially abundant features |
Differential abundance testing with ANCOM from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/ |
| feature_table_visualizations | qiime2 create feature visual summaries |
FeatureTable and FeatureData summaries from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/ |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| dada2_table | File | ||
| rooted_tree | File | ||
| unrooted_tree | File | ||
| filter_table_file | File | ||
| taxa_barplot_file | File | ||
| taxonomy_artifact | File | ||
| collapsed_table_file | File | ||
| dada2_denoising_stats | File | ||
| comp_gut_table_l6_file | File | ||
| composition_table_file | File | ||
| ancom_visualization_file | File | ||
| taxonomy_visualization_file | File | ||
| dada2_visualization_artifact | File | ||
| dada2_representative_sequences | File | ||
| masked_representative_sequences | File | ||
| aligned_representative_sequences | File | ||
| ancom_subject_16_visualization_file | File | ||
| feature_table_summarize_visualization | File | ||
| feature_table_tabulation_visualization | File |
Permalink:
https://w3id.org/cwl/view/git/ef08cb00bd55b4c712645d171dbc691e01ed6165/packed/qiime2-step2-dada2.cwl?part=main
