Workflow: qiime2 Deblur detect/correct sequence data
Fetched 2023-01-11 05:52:10 GMT
Verified with cwltool version 3.1.20221201130942
Option 2: Deblur from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/
- 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 |
|---|---|---|---|
| trim_length | Integer | ||
| demux_sequences_artifact | File | ||
| demux_filter_visualization_filename | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| deblur_denoise |
../tools/qiime2/deblur-denoise-16S.cwl
(CommandLineTool)
|
qiime2: Perform sequence quality control for Illumina data using the Deblur workflow with a 16S reference as a positive filter | |
| deblur_visualize |
../tools/qiime2/deblur-visualize-stats.cwl
(CommandLineTool)
|
qiime2: Display Deblur statistics per sample | |
| deblur_quality_filter |
../tools/qiime2/quality-filter-q-score.cwl
(CommandLineTool)
|
qiime2: Filter sequences based on quality scores and the presence of ambiguous base calls | |
| deblur_metadata_tabulate |
../tools/qiime2/metadata-tabulate.cwl
(CommandLineTool)
|
qiime2: Generate a tabular view of metadata |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| stats | File | ||
| table | File | ||
| rep_seqs | File | ||
| filter_stats | File | ||
| demux_filter_stats | File | ||
| filtered_sequences | File | ||
| stats_visualization | File |
Permalink:
https://w3id.org/cwl/view/git/a6a7d5bd034f8ccf01b809bc9f5ecf87e5c5652c/subworkflows/qiime2-03-deblur.cwl
