Workflow: EMG pipeline v3.0 (paired end version)
Fetched 2023-01-08 23:44:13 GMT
Verified with cwltool version 3.1.20221201130942
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| 5S_model | File [HMMER format] | ||
| 16S_model | File [HMMER format] | ||
| 23S_model | File [HMMER format] | ||
| tRNA_model | File [HMMER format] | ||
| forward_reads | File [FASTQ] | ||
| reverse_reads | File [FASTQ] | ||
| go_summary_config | File | ||
| fraggenescan_model | https://w3id.org/cwl/view/git/ca6ca613f0d3728d9589a6ca6293e66dfde87bfb/tools/FragGeneScan-model.yaml#model |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| overlap_reads |
../tools/seqprep.cwl
(CommandLineTool)
|
||
| unified_processing |
emg-pipeline-v3.cwl
(Workflow)
|
EMG pipeline v3.0 (single end version) | |
| combine_overlaped_and_unmerged_reads |
../tools/seqprep-merge.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| tree | File | ||
| biom_json | File | ||
| predicted_CDS | File | ||
| otu_table_summary | File | ||
| processed_sequences | File | ||
| functional_annotations | File |
Permalink:
https://w3id.org/cwl/view/git/ca6ca613f0d3728d9589a6ca6293e66dfde87bfb/workflows/emg-pipeline-v3-paired.cwl
