Workflow Type: Galaxy
Frozen
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 |
|
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 |
|
list_of_lists_of_preprocessed_samples | list_of_lists_of_preprocessed_samples | n/a |
|
splitted_extracted_samples_IDs | splitted_extracted_samples_IDs | n/a |
|
flye_consensus_fasta | flye_consensus_fasta | n/a |
|
flye_assembly_graph | flye_assembly_graph | n/a |
|
flye_assembly_gfa | flye_assembly_gfa | n/a |
|
flye_assembly_info_tabular | flye_assembly_info_tabular | n/a |
|
parsed_extracted_samples_IDs_to_text | parsed_extracted_samples_IDs_to_text | n/a |
|
medaka_gaps_in_draft_bed_file | medaka_gaps_in_draft_bed_file | n/a |
|
medaka_log_file | medaka_log_file | n/a |
|
medaka_propability_h5_file | medaka_propability_h5_file | n/a |
|
medaka_calls_of_draft_bam_file | medaka_calls_of_draft_bam_file | n/a |
|
sample_all_contigs | sample_all_contigs | n/a |
|
bandage_assembly_graph_image | bandage_assembly_graph_image | n/a |
|
sample_specific_contigs_tabular_file_preparation | sample_specific_contigs_tabular_file_preparation | n/a |
|
abricate_with_vfdb_to_identify_genes_with_VFs | abricate_with_vfdb_to_identify_genes_with_VFs | n/a |
|
abricate_report_using_ncbi_database_to_indentify_amr | abricate_report_using_ncbi_database_to_indentify_amr | n/a |
|
sample_specific_contigs_tabular_file | sample_specific_contigs_tabular_file | n/a |
|
vfs | vfs | n/a |
|
amrs | amrs | n/a |
|
contigs | contigs | n/a |
|
Version History
v0.1 (earliest) Created 7th Sep 2024 at 03:03 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
f9f8f4b
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Created: 7th Sep 2024 at 03:03
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