Workflow: QIIME2 Step 2 (DADA2 option)
Fetched 2024-05-18 16:40:45 GMT
Verified with cwltool version 3.1.20221201130942
QIIME2 DADA2, feature summaries, phylogenetic diversity tree, taxonomic analysis and ancom
- Selected
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- Default Values
- Nested Workflows
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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 |
|---|---|---|---|
| sample_metadata | File | ||
| dada2_trim_left_f | Integer | ||
| dada2_trim_left_r | Integer | ||
| dada2_trunc_len_f | Integer | ||
| dada2_trunc_len_r | Integer | ||
| taxonomy_filename | String | ||
| dada2_stats_filename | String | ||
| dada2_table_filename | String | ||
| rooted_tree_filename | String | ||
| taxonomic_classifier | File | ||
| output_filename_prefix | String | ||
| unrooted_tree_filename | String | ||
| dada2_denoise_n_threads | Integer | ||
| taxa_bar_plots_filename | String | ||
| demux_sequences_artifact | File | ||
| aligned_rep_seqs_filename | String | ||
| filter_feature_table_where | String | ||
| dada2_denoising_stats_filename | String | ||
| feature_table_summary_filename | String | ||
| taxonomy_visualization_filename | String | ||
| filtered_table_filename_filename | String | ||
| masked_aligned_rep_seqs_filename | String | ||
| feature_table_tabulation_filename | String | ||
| dada2_representative_sequences_filename | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| dada2_sequences |
subworkflows/qiime2-03-dada2-paired.cwl
(Workflow)
|
qiime2 DADA2 detect/correct paired sequence data |
Option 1: DADA2 from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/ |
| phylogenetic_tree |
subworkflows/qiime2-05-phylogeny.cwl
(Workflow)
|
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/ |
|
| feature_table_visualizations |
subworkflows/qiime2-04-features.cwl
(Workflow)
|
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 | ||
| taxa_barplot_file | File | ||
| taxonomy_artifact | File | ||
| dada2_denoising_stats | File | ||
| taxonomy_visualization_file | File | ||
| dada2_visualization_artifact | File | ||
| dada2_representative_sequences | File | ||
| filtered_feature_table_artifact | File | ||
| masked_representative_sequences | File | ||
| aligned_representative_sequences | File | ||
| feature_table_summarize_visualization | File | ||
| feature_table_tabulation_visualization | File |
Permalink:
https://w3id.org/cwl/view/git/a6a7d5bd034f8ccf01b809bc9f5ecf87e5c5652c/16s-step2-dada2-paired.cwl
