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

Workflow Type: Galaxy

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

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
help Creators and Submitter
Creators
  • Engy Nasr
  • Bérénice Batut
  • Paul Zierep
Submitter
Citation
Nasr, E., Batut, B., & Zierep, P. (2024). gene-based-pathogen-identification/main. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.1062.1
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Views: 1036   Downloads: 212   Runs: 0

Created: 26th Jun 2024 at 03:02

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