Workflow: blastp_wnode_naming

Fetched 2022-09-23 06:30:31 GMT
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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 (Optional)
soft_masking String (Optional)
top_by_score Integer (Optional)
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 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/5282690e0f634a5f83107ba878fe62cbbb347408/task_types/tt_blastp_wnode_naming.cwl