Workflow: PGAP Pipeline, simple user input, PGAPX-134

Fetched 2023-01-04 19:12:54 GMT

PGAP pipeline for external usage, powered via containers, simple user input: (FASTA + yaml only, no template)

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Inputs

ID Type Title Doc
fasta File
submol File
uuid_in File (Optional)
make_uuid Boolean (Optional)
no_internet Boolean (Optional)
gc_assm_name String
report_usage Boolean
ignore_all_errors Boolean (Optional)
supplemental_data Directory
blast_hits_cache_data Directory (Optional)

Steps

ID Runs Label Doc
fastaval
progs/fastaval.cwl (CommandLineTool)
fastaval
passdata
e0bcf37908bde249b2b3e568d28e7a96 (ExpressionTool)
standard_pgap
wf_common.cwl (Workflow)
PGAP Pipeline

PGAP pipeline for external usage, powered via containers

prepare_input_template Prepare user input

Prepare user input for NCBI-PGAP pipeline

Outputs

ID Type Label Doc
gbk File
gff File
sqn File
calls File
input_fasta File
input_submol File
protein_fasta File (Optional)
nucleotide_fasta File (Optional)
final_asnval_error_diag File (Optional)
final_asndisc_error_diag File (Optional)
initial_asnval_error_diag File (Optional)
initial_asndisc_error_diag File (Optional)
Permalink: https://w3id.org/cwl/view/git/7cee09fb3e33c851e4e1dfc965c558b82290a785/pgap.cwl