CWL Workflow: assembly-wf--v.5-cond.cwl

This workflow is Open Source and may be reused according to the terms of: Apache License 2.0

Note that the tools invoked by the workflow may have separate licenses.

Inputs

ID	Type	Title	Doc
graphs	String
lsu_db	File
ssu_db	File
contigs	File
ko_file	String
lsu_tax	String
ssu_tax	String
lsu_otus	String
ssu_otus	String
EggNOG_db	String
fgs_train	String
go_config	String
lsu_label	String
ssu_label	String
5s_pattern	String
CGC_config	String
ips_header	String
rfam_models	String[]
5.8s_pattern	String
CGC_postfixes	String[]
cgc_chunk_size	Integer
diamond_header	String
pathways_names	String
EggNOG_data_dir	String
Uniref90_db_txt	String
genecaller_order	String
hmmsearch_header	String
pathways_classes	String
rfam_model_clans	String
EggNOG_diamond_db	String
HMM_name_database	String
clusters_glossary	String
contig_min_length	Integer
gp_flatfiles_path	String
HMM_omit_alignment	Boolean
func_ann_names_ips	String
other_ncrna_models	String[]
diamond_databaseFile	String
func_ann_names_hmmer	String
diamond_maxTargetSeqs	Integer
InterProScan_databases	String
protein_chunk_size_IPS	Integer
protein_chunk_size_hmm	Integer
HMM_gathering_bit_score	Boolean
InterProScan_applications	String[]
InterProScan_outputFormat	String[]
protein_chunk_size_eggnog	Integer

ID	Runs	Label	Doc
after-qc	conditionals/assembly/assembly-2.cwl (Workflow)
before-qc	conditionals/assembly/assembly-1.cwl (Workflow)
touch_file_flag	../utils/touch_file.cwl (CommandLineTool)
touch_no_cds_flag	../utils/touch_file.cwl (CommandLineTool)

ID	Type	Label	Doc
stats	Directory (Optional)
qc-status	File
rna-count	File (Optional)
qc_summary	File
bgzip_index	File (Optional)
hashsum_input	File
bgzip_fasta_file	File (Optional)
compressed_files	File[]
index_fasta_file	File (Optional)
no_cds_flag_file	File (Optional)
no_tax_flag_file	File (Optional)
chunking_proteins	File[] (Optional)
completed_flag_file	File (Optional)
chunking_nucleotides	File[] (Optional)
qc-statistics_folder	Directory
pathways_systems_folder	Directory (Optional)
taxonomy-summary_folder	Directory (Optional)
functional_annotation_folder	Directory (Optional)
sequence-categorisation_folder	Directory (Optional)
pathways_systems_folder_antismash	Directory (Optional)
pathways_systems_folder_antismash_summary	Directory (Optional)