Workflow: deal_with_functional_annotation.cwl
Fetched 2025-11-11 13:32:28 GMT
Verified with cwltool version 3.1.20230201224320
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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 |
|---|---|---|---|
| cds | File | ||
| rna | File | ||
| fasta | File | ||
| ko_file | String | ||
| IPS_table | File | ||
| go_config | String | ||
| ips_header | String | ||
| diamond_table | File | ||
| hmmscan_table | File | ||
| output_gff_gz | File | ||
| diamond_header | String | ||
| eggnog_orthologs | File | ||
| hmmsearch_header | String | ||
| output_gff_index | File | ||
| eggnog_annotations | File | ||
| antismash_geneclusters_txt | File (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| pfam |
/cwl/view/git/49ae257c560e71d2946290d1705b2912fd81f76f/tools/Pfam-Parse/pfam_annotations.cwl
(CommandLineTool)
|
Parse Pfam hits from Interpro annotation output | |
| go_summary |
/cwl/view/git/49ae257c560e71d2946290d1705b2912fd81f76f/tools/GO-slim/go_summary.cwl
(CommandLineTool)
|
||
| chunking_tsv |
/cwl/view/git/49ae257c560e71d2946290d1705b2912fd81f76f/utils/result-file-chunker/result_chunker.cwl
(CommandLineTool)
|
||
| header_addition |
/cwl/view/git/49ae257c560e71d2946290d1705b2912fd81f76f/utils/add_header/add_header.cwl
(CommandLineTool)
|
||
| write_summaries |
../func_summaries.cwl
(Workflow)
|
||
| compression_func_ann |
/cwl/view/git/49ae257c560e71d2946290d1705b2912fd81f76f/utils/pigz/gzip.cwl
(CommandLineTool)
|
||
| move_to_functional_annotation_folder |
/cwl/view/git/49ae257c560e71d2946290d1705b2912fd81f76f/utils/return_directory.cwl
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| stats | Directory | ||
| summary_antismash | File (Optional) | ||
| functional_annotation_folder | Directory |
Permalink:
https://w3id.org/cwl/view/git/49ae257c560e71d2946290d1705b2912fd81f76f/workflows/subworkflows/assembly/deal_with_functional_annotation.cwl
