Workflow: assm_assm_blastn_wnode
Fetched 2023-01-09 01:22:30 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
https://raw.githubusercontent.com/ncbi/pgap/664e99a23a3ed4ba36c08323ac597c4fbcd88df1/LICENSE.md
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| task | String | ||
| evalue | Float (Optional) | ||
| compart | Boolean (Optional) | ||
| gapopen | Integer (Optional) | ||
| affinity | String | ||
| asn_cache | Directory | ||
| gapextend | Integer (Optional) | ||
| nogenbank | Boolean (Optional) | ||
| word_size | Integer (Optional) | ||
| gencoll_asn | File | ||
| window_size | Integer (Optional) | ||
| merge_engine | String (Optional) | ||
| soft_masking | String (Optional) | ||
| max_target_seqs | Integer (Optional) | ||
| ref_gencoll_asn | File | ||
| workers_per_cpu | Float (Optional) | ||
| max_bases_per_call | Integer (Optional) | ||
| merge_align_filter | String (Optional) | ||
| queries_gc_id_list | File | ||
| subjects_gc_id_list | File | ||
| use_common_components | Boolean |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| gpx_qdump |
../progs/gpx_qdump.cwl
(CommandLineTool)
|
gpx_qdump | |
| gpx_qsubmit |
../progs/gpx_qsubmit.cwl
(CommandLineTool)
|
gpx_qsubmit |
This workflow is specialized for the case when there is an LDS2 input LDS2 is a _reference_ object, the kind that CWL does not like we need to provide actual input: proteins which matches the name of ASN.1 object references in LDS2 Another limitation is that it can handle no more than two item arrays in blastdb_dir and asn_cache Workaround used so far: in: proteins: default: class: File path: '/dev/null' basename: 'null' contents: '' |
| assm_assm_blastn_wnode |
../progs/assm_assm_blastn_wnode.cwl
(CommandLineTool)
|
assm_assm_blastn_wnode | |
| assm_assm_blastn_create_jobs |
../progs/assm_assm_blastn_create_jobs.cwl
(CommandLineTool)
|
assm_assm_blastn_create_jobs |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| blast_align | File |
Permalink:
https://w3id.org/cwl/view/git/664e99a23a3ed4ba36c08323ac597c4fbcd88df1/task_types/tt_assm_assm_blastn_wnode.cwl
