Workflow: blastp_wnode_struct

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


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

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: ''


ID Type Label Doc
blast_align File[]