Workflow: blastp_wnode_struct

Fetched 2021-11-30 00:14:44 GMT
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Inputs

ID Type Title Doc
asn_cache Directory[]
dbsize String
top_by_score Integer
taxon_db File
ofmt String
threshold Integer
max_target_seqs Integer
allow_intersection Boolean
blastdb String[]
compart Boolean
seg String
taxid Integer
proteins File
word_size Integer
no_merge Boolean
max_jobs Integer
align_filter String
blastdb_dir Directory
lds2 File
comp_based_stats String
blast_hits_cache File (Optional)
nogenbank Boolean
evalue Float (Optional)
scatter_gather_nchunks String
batch-size Integer (Optional)
max_batch_length Integer
extra_coverage Integer (Optional)
ids File[]
genus_list Integer[]
soft_masking String
blast_type String (Optional)
affinity String

Steps

ID Runs Label Doc
split_jobs
../split_jobs/split.cwl (CommandLineTool)
cwl split wrapper
collect_aligns
../split_jobs/cat_array_of_files.cwl (CommandLineTool)
file concatenation
cluster_and_qdump cluster_blastp_wnode and gpx_qdump combined
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: ''

Outputs

ID Type Label Doc
blast_align File[]
Permalink: https://w3id.org/cwl/view/git/a402541b8530f30eab726c160da90a23036847a1/task_types/tt_blastp_wnode_struct.cwl