- 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/5463361069e263ad6455858e054c1337b1d9e752/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/5463361069e263ad6455858e054c1337b1d9e752/task_types/tt_blastn_wnode.cwl