CWL Workflow: assembly-2.cwl

Workflow: assembly-2.cwl

Fetched 2024-05-09 23:50:10 GMT

Verified with cwltool version 3.1.20230201224320

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.

ID	Type	Title	Doc
graphs	String
lsu_db	File
ssu_db	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
filtered_fasta	File
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
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
cgc	../../subworkflows/assembly/CGC-subwf.cwl (Workflow)
antismash	/cwl/view/git/a83ee883bb3c7480010fa952939fac771491ddf4/tools/Assembly/antismash/chunking_antismash_with_conditionals/wf_antismash.cwl (Workflow)	WF leaves sequences that length is more than 1000bp, run antismash + gene clusters post-processing, GFF generation
compression	/cwl/view/git/a83ee883bb3c7480010fa952939fac771491ddf4/utils/pigz/gzip.cwl (CommandLineTool)
fasta_index	/cwl/view/git/a83ee883bb3c7480010fa952939fac771491ddf4/tools/Assembly/index_fasta/fasta_index.cwl (CommandLineTool)
other_ncrnas	../../subworkflows/other_ncrnas.cwl (Workflow)	extract other ncrnas!
chunking_final	../../subworkflows/final_chunking.cwl (Workflow)
return_tax_dir	/cwl/view/git/a83ee883bb3c7480010fa952939fac771491ddf4/utils/return_directory.cwl (ExpressionTool)
rna_prediction	../../subworkflows/rna_prediction-sub-wf.cwl (Workflow)
no_tax_file_flag	/cwl/view/git/a83ee883bb3c7480010fa952939fac771491ddf4/utils/touch_file.cwl (CommandLineTool)
move_to_seq_cat_folder	/cwl/view/git/a83ee883bb3c7480010fa952939fac771491ddf4/utils/return_directory.cwl (ExpressionTool)
functional_annotation_and_post_processing	../../subworkflows/assembly/func_ann_and_post_processing-subwf.cwl (Workflow)

ID	Type	Label	Doc
stats	Directory (Optional)
count_CDS	Integer
rna-count	File
bgzip_index	File
bgzip_fasta_file	File
compressed_files	File[]
index_fasta_file	File
chunking_proteins	File[] (Optional)
chunking_nucleotides	File[] (Optional)
optional_tax_file_flag	File (Optional)
pathways_systems_folder	Directory (Optional)
taxonomy-summary_folder	Directory
functional_annotation_folder	Directory (Optional)
sequence-categorisation_folder	Directory
pathways_systems_folder_antismash	Directory
pathways_systems_folder_antismash_summary	Directory (Optional)

Permalink: https://w3id.org/cwl/view/git/a83ee883bb3c7480010fa952939fac771491ddf4/workflows/conditionals/assembly/assembly-2.cwl