Workflow: assembly-2.cwl
Fetched 2026-06-06 16:38:06 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
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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 |
|---|---|---|---|
| graphs | String | ||
| lsu_db | File | ||
| ssu_db | File | ||
| ko_file | String | ||
| lsu_tax | String | ||
| ssu_tax | String | ||
| lsu_otus | String | ||
| ssu_otus | String | ||
| EggNOG_db | String | ||
| fgs_train | String | ||
| go_config | String | ||
| lsu_label | String | ||
| ssu_label | String | ||
| 5s_pattern | String | ||
| CGC_config | String | ||
| ips_header | String | ||
| rfam_models | String[] | ||
| 5.8s_pattern | String | ||
| CGC_postfixes | String[] | ||
| cgc_chunk_size | Integer | ||
| diamond_header | String | ||
| filtered_fasta | File | ||
| pathways_names | String | ||
| EggNOG_data_dir | String | ||
| Uniref90_db_txt | String | ||
| genecaller_order | String | ||
| hmmsearch_header | String | ||
| pathways_classes | String | ||
| rfam_model_clans | String | ||
| EggNOG_diamond_db | String | ||
| HMM_name_database | String | ||
| clusters_glossary | String | ||
| gp_flatfiles_path | String | ||
| HMM_omit_alignment | Boolean | ||
| func_ann_names_ips | String | ||
| other_ncrna_models | String[] | ||
| diamond_databaseFile | String | ||
| func_ann_names_hmmer | String | ||
| diamond_maxTargetSeqs | Integer | ||
| InterProScan_databases | String | ||
| protein_chunk_size_IPS | Integer | ||
| protein_chunk_size_hmm | Integer | ||
| HMM_gathering_bit_score | Boolean | ||
| InterProScan_applications | String[] | ||
| InterProScan_outputFormat | String[] | ||
| protein_chunk_size_eggnog | Integer |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| cgc |
../../subworkflows/assembly/CGC-subwf.cwl
(Workflow)
|
||
| antismash | WF leaves sequences that length is more than 1000bp, run antismash + gene clusters post-processing, GFF generation | ||
| compression |
/cwl/view/git/fff6fa392370b56e1fe7c374167ba73df3018775/utils/pigz/gzip.cwl
(CommandLineTool)
|
||
| fasta_index |
/cwl/view/git/fff6fa392370b56e1fe7c374167ba73df3018775/tools/Assembly/index_fasta/fasta_index.cwl
(CommandLineTool)
|
||
| other_ncrnas |
../../subworkflows/other_ncrnas.cwl
(Workflow)
|
extract other ncrnas! | |
| chunking_final |
../../subworkflows/final_chunking.cwl
(Workflow)
|
||
| return_tax_dir |
/cwl/view/git/fff6fa392370b56e1fe7c374167ba73df3018775/utils/return_directory.cwl
(ExpressionTool)
|
||
| rna_prediction |
../../subworkflows/rna_prediction-sub-wf.cwl
(Workflow)
|
||
| no_tax_file_flag |
/cwl/view/git/fff6fa392370b56e1fe7c374167ba73df3018775/utils/touch_file.cwl
(CommandLineTool)
|
||
| move_to_seq_cat_folder |
/cwl/view/git/fff6fa392370b56e1fe7c374167ba73df3018775/utils/return_directory.cwl
(ExpressionTool)
|
||
| functional_annotation_and_post_processing |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| stats | Directory (Optional) | ||
| count_CDS | Integer | ||
| rna-count | File | ||
| bgzip_index | File | ||
| bgzip_fasta_file | File | ||
| compressed_files | File[] | ||
| index_fasta_file | File | ||
| chunking_proteins | File[] (Optional) | ||
| chunking_nucleotides | File[] (Optional) | ||
| optional_tax_file_flag | File (Optional) | ||
| pathways_systems_folder | Directory (Optional) | ||
| taxonomy-summary_folder | Directory | ||
| functional_annotation_folder | Directory (Optional) | ||
| sequence-categorisation_folder | Directory | ||
| pathways_systems_folder_antismash | Directory | ||
| pathways_systems_folder_antismash_summary | Directory (Optional) |
Permalink:
https://w3id.org/cwl/view/git/fff6fa392370b56e1fe7c374167ba73df3018775/workflows/conditionals/assembly/assembly-2.cwl
