Workflow: workflow_mock_ngtax.cwl
Fetched 2023-01-03 19:15:37 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| mock3 | String (Optional) | Mock3 reference |
Mock3 reference selection |
| mock4 | String (Optional) | Mock4 reference |
Mock4 reference selection |
| sample | String | Sample name |
Name of the sample being analysed |
| fragment | String | Subfragment name |
Subfragment that is being analysed (e.g. V1-V3 or V5-region) |
| metadata | File (Optional) | Metadata file |
UNLOCK assay metadata file |
| destination | String (Optional) | Output Destination |
Optional Output destination used for cwl-prov reporting. |
| for_read_len | Integer | Reverse read length |
Read length of the reverse read |
| reference_db | String (Optional) | Reference database |
Reference database used in FASTA format |
| rev_read_len | Integer (Optional) | Reverse read length |
Read length of the reverse read |
| forward_primer | String | Forward primer |
Forward primer used |
| reverse_primer | String (Optional) | Reverse primer |
Reverse primer used |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| ngtax |
../ngtax/ngtax.cwl
(CommandLineTool)
|
NGTax amplicon analysis |
Runs NGTAX amplicon analysis |
| ngtax_to_tsv-fasta |
../ngtax/ngtax_to_tsv-fasta.cwl
(CommandLineTool)
|
NGtax2 output conversion to prepare for biom file and ASV fasta file |
|
| ngtax_files_to_folder |
../expressions/files_to_folder.cwl
(ExpressionTool)
|
Transforms the input files to a mentioned directory |
|
| phyloseq_files_to_folder |
../expressions/files_to_folder.cwl
(ExpressionTool)
|
Transforms the input files to a mentioned directory |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| files_to_folder_ngtax | Directory | ||
| files_to_folder_phyloseq | Directory |
Permalink:
https://w3id.org/cwl/view/git/b9097b82e6ab6f2c9496013ce4dd6877092956a0/cwl/workflows/workflow_mock_ngtax.cwl
