gene-based-pathogen-identification/main
v0.1

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Workflow Type: Galaxy

Nanopore datasets analysis - Phylogenetic Identification - antibiotic resistance genes detection and contigs building

SEEK ID: https://workflowhub.eu/workflows/1062?version=1

DOI: 10.48546/workflowhub.workflow.1062.1

Inputs

ID	Name	Description	Type
collection_of_preprocessed_samples	collection_of_preprocessed_samples	Output collection from the Nanopore Preprocessing workflow	File[]

Steps

ID	Name	Description
1	Extract element identifiers	toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2
2	Build list	__BUILD_LIST__
3	Split file	toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0
4	Flye	toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0
5	Parse parameter value	param_value_from_file
6	medaka consensus pipeline	toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy0
7	Bandage Image	toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
8	Compose text parameter value	toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
9	FASTA-to-Tabular	toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1
10	ABRicate	toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.0.1
11	ABRicate	toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.0.1
12	Replace	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4
13	Replace	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4
14	Replace	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4
15	Tabular-to-FASTA	toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1

Outputs

ID	Name	Description	Type
extracted_samples_IDs	extracted_samples_IDs	n/a	File
list_of_lists_of_preprocessed_samples	list_of_lists_of_preprocessed_samples	n/a	File
splitted_extracted_samples_IDs	splitted_extracted_samples_IDs	n/a	File
flye_consensus_fasta	flye_consensus_fasta	n/a	File
flye_assembly_graph	flye_assembly_graph	n/a	File
flye_assembly_gfa	flye_assembly_gfa	n/a	File
flye_assembly_info_tabular	flye_assembly_info_tabular	n/a	File
parsed_extracted_samples_IDs_to_text	parsed_extracted_samples_IDs_to_text	n/a	File
medaka_gaps_in_draft_bed_file	medaka_gaps_in_draft_bed_file	n/a	File
medaka_log_file	medaka_log_file	n/a	File
medaka_propability_h5_file	medaka_propability_h5_file	n/a	File
medaka_calls_of_draft_bam_file	medaka_calls_of_draft_bam_file	n/a	File
sample_all_contigs	sample_all_contigs	n/a	File
bandage_assembly_graph_image	bandage_assembly_graph_image	n/a	File
sample_specific_contigs_tabular_file_preparation	sample_specific_contigs_tabular_file_preparation	n/a	File
abricate_with_vfdb_to_identify_genes_with_VFs	abricate_with_vfdb_to_identify_genes_with_VFs	n/a	File
abricate_report_using_ncbi_database_to_indentify_amr	abricate_report_using_ncbi_database_to_indentify_amr	n/a	File
sample_specific_contigs_tabular_file	sample_specific_contigs_tabular_file	n/a	File
vfs	vfs	n/a	File
amrs	amrs	n/a	File
contigs	contigs	n/a	File

Version History

v0.1 (earliest) Created 26th Jun 2024 at 03:02 by WorkflowHub Bot

Updated to v0.1

Frozen v0.1 f9f8f4b

Creators and Submitter

Creators

Engy Nasr
Bérénice Batut
Paul Zierep

Submitter

WorkflowHub Bot

Tools

Flye

Medaka

Bandage

ABRicate

Citation

Nasr, E., Batut, B., & Zierep, P. (2024). gene-based-pathogen-identification/main. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.1062.1

License

MIT License

Activity

Views: 3224 Downloads: 1213 Runs: 2

Created: 26th Jun 2024 at 03:02

gene-based-pathogen-identification/main v0.1