Workflow: tt_blastn_wnode
Fetched 2023-01-10 23:07:01 GMT
Verified with cwltool version 3.1.20221201130942
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This workflow is Open Source and may be reused according to the terms of:
https://raw.githubusercontent.com/ncbi/pgap/001fab592188cb525afa1c4db6226b833faec106/LICENSE.md
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| dust | String (Optional) | ||
| task | String (Optional) | ||
| evalue | Float | ||
| blastdb | String | ||
| ids_out | File | ||
| affinity | String (Optional) | ||
| asn_cache | Directory | ||
| word_size | Integer | ||
| blastdb_dir | Directory | ||
| soft_masking | String (Optional) | ||
| perc_identity | Float (Optional) | ||
| max_target_seqs | Integer (Optional) | ||
| max_batch_length | Integer (Optional) | ||
| best_hit_overhang | Float (Optional) | ||
| best_hit_score_edge | Float (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| 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: '' |
| blastn_wnode |
../progs/blastn_wnode.cwl
(CommandLineTool)
|
blastn_wnode | |
| gpx_make_outputs |
../progs/gpx_make_outputs.cwl
(CommandLineTool)
|
gpx_make_outputs |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| blast_align | File |
Permalink:
https://w3id.org/cwl/view/git/001fab592188cb525afa1c4db6226b833faec106/task_types/tt_blastn_wnode.cwl
