- 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/d39017c63dd8e088f1ad3809d709529df602e05f/LICENSE.md
Note that the tools invoked by the workflow may have separate licenses.
Inputs
ID | Type | Title | Doc |
---|---|---|---|
ids | File[] | ||
seg | String | ||
lds2 | File | ||
ofmt | String | ||
taxid | Integer | ||
dbsize | String | ||
evalue | Float (Optional) | ||
blastdb | String[] | ||
compart | Boolean | ||
affinity | String | ||
max_jobs | Integer | ||
no_merge | Boolean | ||
proteins | File | ||
taxon_db | File | ||
asn_cache | Directory[] | ||
nogenbank | Boolean | ||
threshold | Integer | ||
word_size | Integer | ||
batch-size | Integer (Optional) | ||
blast_type | String (Optional) | ||
genus_list | Integer[] | ||
blastdb_dir | Directory | ||
align_filter | String | ||
soft_masking | String | ||
top_by_score | Integer | ||
extra_coverage | Integer (Optional) | ||
max_target_seqs | Integer | ||
blast_hits_cache | File (Optional) | ||
comp_based_stats | String | ||
max_batch_length | Integer | ||
allow_intersection | Boolean | ||
scatter_gather_nchunks | String |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
split_jobs |
../split_jobs/split.cwl
(CommandLineTool)
|
cwl split wrapper | |
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: '' |
collect_aligns |
../split_jobs/cat_array_of_files.cwl
(CommandLineTool)
|
file concatenation | |
cluster_and_qdump |
tt_cluster_and_qdump.cwl
(Workflow)
|
cluster_blastp_wnode and gpx_qdump combined | |
retrieve_cached_hits |
../progs/orf_hits_cache_retrieve.cwl
(CommandLineTool)
|
orf_hits_cache_retrieve |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
blast_align | File[] |
Permalink:
https://w3id.org/cwl/view/git/d39017c63dd8e088f1ad3809d709529df602e05f/task_types/tt_blastp_wnode_naming.cwl