Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation
2.0

Workflow Type: Galaxy

Pathogens of all samples report generation and visualization

Associated Tutorial

This workflows is part of the tutorial Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition, available in the GTN

Features

Thanks to...

Workflow Author(s): Engy Nasr, Bérénice Batut, Paul Zierep

Tutorial Author(s): Bérénice Batut, Engy Nasr, Paul Zierep

Tutorial Contributor(s): Hans-Rudolf Hotz, Wolfgang Maier, Saskia Hiltemann, Deepti Varshney, Paul Zierep, Bérénice Batut, Björn Grüning, Cristóbal Gallardo, Engy Nasr, Helena Rasche

Grants(s): Gallantries: Bridging Training Communities in Life Science, Environment and Health, EOSC-Life

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
amr_identified_by_ncbi amr_identified_by_ncbi output_of_abricate_with_amrfinderncbi
  • File[]
amrs amrs amrs
  • File[]
contigs contigs Contigs
  • File[]
mapping_coverage_percentage_per_sample mapping_coverage_percentage_per_sample mapping_coverage_percentage_per_sample
  • File
mapping_mean_depth_per_sample mapping_mean_depth_per_sample mapping_mean_depth_per_sample
  • File
metadata metadata samples_metadata
  • File?
number_of_variants_per_sample number_of_variants_per_sample number_of_variants_per_sample
  • File
removed_hosts_percentage_tabular removed_hosts_percentage_tabular removed_hosts_percentage_tabular
  • File
vfs vfs VFs
  • File[]
vfs_of_genes_identified_by_vfdb vfs_of_genes_identified_by_vfdb output_of_abricate_with_vfdb
  • File[]

Steps

ID Name Description
10 Filter failed datasets __FILTER_FAILED_DATASETS__
11 Filter failed datasets __FILTER_FAILED_DATASETS__
12 Bar chart barchart_gnuplot
13 Bar chart barchart_gnuplot
14 Bar chart barchart_gnuplot
15 Filter failed datasets __FILTER_FAILED_DATASETS__
16 Bar chart barchart_gnuplot
17 Bar chart barchart_gnuplot
18 Filter failed datasets __FILTER_FAILED_DATASETS__
19 Filter failed datasets __FILTER_FAILED_DATASETS__
20 Remove beginning Remove beginning1
21 Remove beginning Remove beginning1
22 Remove beginning Remove beginning1
23 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
24 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
25 Remove beginning Remove beginning1
26 Count Count1
27 Count Count1
28 Group Grouping1
29 Unique toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1
30 Split by group toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.6
31 Unique toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1
32 Cut Cut1
33 Cut Cut1
34 Filter empty datasets __FILTER_EMPTY_DATASETS__
35 Cut Cut1
36 Cut Cut1
37 Cut Cut1
38 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
39 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
40 Column join toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3
41 bedtools getfasta toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1
42 Remove beginning Remove beginning1
43 bedtools getfasta toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1
44 Column Regex Find And Replace toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3
45 Column Regex Find And Replace toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3
46 Column Regex Find And Replace toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3
47 Regex Find And Replace toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3
48 bedtools getfasta toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1
49 Regex Find And Replace toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3
50 Multi-Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/9.3+galaxy1
51 Heatmap w ggplot toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap/ggplot2_heatmap/3.4.0+galaxy0
52 Filter empty datasets __FILTER_EMPTY_DATASETS__
53 ClustalW toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1+galaxy1
54 Filter empty datasets __FILTER_EMPTY_DATASETS__
55 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1
56 FASTA-to-Tabular toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1
57 Filter empty datasets __FILTER_EMPTY_DATASETS__
58 FASTA-to-Tabular toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1
59 Cut Cut1
60 FASTTREE toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1
61 Cut Cut1
62 Group Grouping1
63 Newick Display toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6+galaxy1
64 Group Grouping1
65 Tabular-to-FASTA toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1
66 Tabular-to-FASTA toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1
67 FASTA Merge Files and Filter Unique Sequences toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0
68 FASTA Merge Files and Filter Unique Sequences toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0
69 ClustalW toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1+galaxy1
70 ClustalW toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1+galaxy1
71 FASTTREE toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1
72 FASTTREE toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1
73 Newick Display toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6+galaxy1
74 Newick Display toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6+galaxy1

Outputs

ID Name Description Type
number_of_reads_before_host_removal_and_number_of_host_reads_found_per_sample_fig number_of_reads_before_host_removal_and_number_of_host_reads_found_per_sample_fig n/a
  • File
removed_host_percentage_fig removed_host_percentage_fig n/a
  • File
mapping_mean_depth_per_sample_fig mapping_mean_depth_per_sample_fig n/a
  • File
mapping_coverage_percentage_per_sample_fig mapping_coverage_percentage_per_sample_fig n/a
  • File
number_of_Variants_and_SNPs_indentified_fig number_of_Variants_and_SNPs_indentified_fig n/a
  • File
all_samples_contigs_in_one_fasta_file all_samples_contigs_in_one_fasta_file n/a
  • File
all_vfs_in_one_tabular all_vfs_in_one_tabular n/a
  • File
split_by_group_collection split_by_group_collection n/a
  • File
adjusted_abricate_vfs_tabular_part1 adjusted_abricate_vfs_tabular_part1 n/a
  • File
adjusted_abricate_vfs_tabular_part2 adjusted_abricate_vfs_tabular_part2 n/a
  • File
amrs_count amrs_count n/a
  • File
vfs_count vfs_count n/a
  • File
heatmap_table heatmap_table n/a
  • File
filtered_sequences_with_vfs_fasta filtered_sequences_with_vfs_fasta n/a
  • File
heatmap_pdf heatmap_pdf n/a
  • File
heatmap_png heatmap_png n/a
  • File
clustalw_on_input_dnd clustalw_on_input_dnd n/a
  • File
clustalw_on_input_clustal clustalw_on_input_clustal n/a
  • File
vfs_amrs_count_table vfs_amrs_count_table n/a
  • File
filtered_empty_datasets filtered_empty_datasets n/a
  • File
fasttree_nhx fasttree_nhx n/a
  • File
newick_genes_tree_graphs_collection newick_genes_tree_graphs_collection n/a
  • File
all_samples_phylogenetic_tree_based_amrs all_samples_phylogenetic_tree_based_amrs n/a
  • File
all_samples_phylogenetic_tree_based_vfs all_samples_phylogenetic_tree_based_vfs n/a
  • File

Version History

2.0 (earliest) Created 2nd Jun 2025 at 10:55 by GTN Bot

Added/updated 4 files


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Created: 2nd Jun 2025 at 10:55

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