Workflows

These workflows are associated with Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Allele-based Pathogen Identification
Engy Nasr, Bérénice Batut, Paul Zierep

Last updated Jun 20, 2024

Launch in Tutorial Mode question
License: MIT
Tests: ✅ Results: Not yet automated

flowchart TD
  0["ℹ️ Input Collection\ncollection_of_preprocessed_samples"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Parameter\nsamples_profile"];
  style 1 fill:#ded,stroke:#393,stroke-width:4px;
  2["ℹ️ Input Dataset\nreference_genome_of_tested_strain"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Convert compressed file to uncompressed."];
  2 -->|output| 3;
  9d6bde4a-7180-4097-9ffd-6992111a617c["Output\ndecompressed_rg_file"];
  3 --> 9d6bde4a-7180-4097-9ffd-6992111a617c;
  style 9d6bde4a-7180-4097-9ffd-6992111a617c stroke:#2c3143,stroke-width:4px;
  4["Map with minimap2"];
  1 -->|output| 4;
  0 -->|output| 4;
  3 -->|output1| 4;
  31779c23-4f26-418e-9418-2551e883dbe7["Output\nmap_with_minimap2"];
  4 --> 31779c23-4f26-418e-9418-2551e883dbe7;
  style 31779c23-4f26-418e-9418-2551e883dbe7 stroke:#2c3143,stroke-width:4px;
  5["Clair3"];
  4 -->|alignment_output| 5;
  3 -->|output1| 5;
  1cf1ee6c-4cb7-45e3-9c7b-88a1b678dd53["Output\nclair3_pileup_vcf"];
  5 --> 1cf1ee6c-4cb7-45e3-9c7b-88a1b678dd53;
  style 1cf1ee6c-4cb7-45e3-9c7b-88a1b678dd53 stroke:#2c3143,stroke-width:4px;
  987f9145-83ab-44f1-801a-b0d527ecbce8["Output\nclair3_full_alignment_vcf"];
  5 --> 987f9145-83ab-44f1-801a-b0d527ecbce8;
  style 987f9145-83ab-44f1-801a-b0d527ecbce8 stroke:#2c3143,stroke-width:4px;
  fab82215-f59a-43b1-92d7-37629a1fdb65["Output\nclair3_merged_output"];
  5 --> fab82215-f59a-43b1-92d7-37629a1fdb65;
  style fab82215-f59a-43b1-92d7-37629a1fdb65 stroke:#2c3143,stroke-width:4px;
  6["Samtools depth"];
  4 -->|alignment_output| 6;
  7["Samtools coverage"];
  4 -->|alignment_output| 7;
  8["bcftools norm"];
  5 -->|merge_output| 8;
  3 -->|output1| 8;
  22553aa1-f5db-4d37-87c4-1164dbb3d2d5["Output\nnormalized_vcf_output"];
  8 --> 22553aa1-f5db-4d37-87c4-1164dbb3d2d5;
  style 22553aa1-f5db-4d37-87c4-1164dbb3d2d5 stroke:#2c3143,stroke-width:4px;
  9["Advanced Cut"];
  6 -->|output| 9;
  10["Remove beginning"];
  7 -->|output| 10;
  11["SnpSift Filter"];
  8 -->|output_file| 11;
  3e7981ec-2205-4571-93eb-10c0dd14b288["Output\nquality_filtered_vcf_output"];
  11 --> 3e7981ec-2205-4571-93eb-10c0dd14b288;
  style 3e7981ec-2205-4571-93eb-10c0dd14b288 stroke:#2c3143,stroke-width:4px;
  12["Table Compute"];
  9 -->|output| 12;
  13["Cut"];
  10 -->|out_file1| 13;
  14["SnpSift Extract Fields"];
  11 -->|output| 14;
  1b0f4f2c-4717-45be-b580-fe10cba78c35["Output\nextracted_fields_from_the_vcf_output"];
  14 --> 1b0f4f2c-4717-45be-b580-fe10cba78c35;
  style 1b0f4f2c-4717-45be-b580-fe10cba78c35 stroke:#2c3143,stroke-width:4px;
  15["bcftools consensus"];
  11 -->|output| 15;
  3 -->|output1| 15;
  49497f3c-9332-4924-bcfd-cb71788ad2c2["Output\nbcftools_consensus"];
  15 --> 49497f3c-9332-4924-bcfd-cb71788ad2c2;
  style 49497f3c-9332-4924-bcfd-cb71788ad2c2 stroke:#2c3143,stroke-width:4px;
  16["Select first"];
  13 -->|out_file1| 16;
  17["Remove beginning"];
  14 -->|output| 17;
  18["Collapse Collection"];
  16 -->|outfile| 18;
  5ee1c158-1a85-45ca-9abd-b30632b3092c["Output\nmapping_coverage_percentage_per_sample"];
  18 --> 5ee1c158-1a85-45ca-9abd-b30632b3092c;
  style 5ee1c158-1a85-45ca-9abd-b30632b3092c stroke:#2c3143,stroke-width:4px;
  19["Count"];
  17 -->|out_file1| 19;
  20["Advanced Cut"];
  18 -->|output| 20;
  21["Cut"];
  19 -->|out_file1| 21;
  22["Paste"];
  20 -->|output| 22;
  12 -->|table| 22;
  25b7b87b-5ef1-487f-90cc-81351a2f81ce["Output\nmapping_mean_depth_per_sample"];
  22 --> 25b7b87b-5ef1-487f-90cc-81351a2f81ce;
  style 25b7b87b-5ef1-487f-90cc-81351a2f81ce stroke:#2c3143,stroke-width:4px;
  23["Select first"];
  21 -->|out_file1| 23;
  24["Collapse Collection"];
  23 -->|outfile| 24;
  25["Column Regex Find And Replace"];
  24 -->|output| 25;
  2852c4ee-24ea-4df7-b59e-54eb6e2f470b["Output\nnumber_of_variants_per_sample"];
  25 --> 2852c4ee-24ea-4df7-b59e-54eb6e2f470b;
  style 2852c4ee-24ea-4df7-b59e-54eb6e2f470b stroke:#2c3143,stroke-width:4px;
	
Gene-based Pathogen Identification
Engy Nasr, Bérénice Batut, Paul Zierep

Last updated Jun 7, 2024

Launch in Tutorial Mode question
License: MIT
Tests: ✅ Results: Not yet automated

flowchart TD
  0["ℹ️ Input Collection\ncollection_of_preprocessed_samples"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Extract element identifiers"];
  0 -->|output| 1;
  d82a93c6-23a9-4f85-879c-ecd759a31087["Output\nextracted_samples_IDs"];
  1 --> d82a93c6-23a9-4f85-879c-ecd759a31087;
  style d82a93c6-23a9-4f85-879c-ecd759a31087 stroke:#2c3143,stroke-width:4px;
  2["Build list"];
  0 -->|output| 2;
  f5b5b256-8ddf-4da8-8111-b1f6d3025a0d["Output\nlist_of_lists_of_preprocessed_samples"];
  2 --> f5b5b256-8ddf-4da8-8111-b1f6d3025a0d;
  style f5b5b256-8ddf-4da8-8111-b1f6d3025a0d stroke:#2c3143,stroke-width:4px;
  3["Split file"];
  1 -->|output| 3;
  eb5317bd-4bad-4cad-9219-3ac379221d6e["Output\nsplitted_extracted_samples_IDs"];
  3 --> eb5317bd-4bad-4cad-9219-3ac379221d6e;
  style eb5317bd-4bad-4cad-9219-3ac379221d6e stroke:#2c3143,stroke-width:4px;
  4["Flye"];
  2 -->|output| 4;
  ff0d8c7b-2ac7-4c6d-a110-f71418dad938["Output\nflye_consensus_fasta"];
  4 --> ff0d8c7b-2ac7-4c6d-a110-f71418dad938;
  style ff0d8c7b-2ac7-4c6d-a110-f71418dad938 stroke:#2c3143,stroke-width:4px;
  2385436f-fbe8-4d77-a40b-27a097d02941["Output\nflye_assembly_graph"];
  4 --> 2385436f-fbe8-4d77-a40b-27a097d02941;
  style 2385436f-fbe8-4d77-a40b-27a097d02941 stroke:#2c3143,stroke-width:4px;
  0e42ce51-c46b-45d8-baa4-45c0e98ac712["Output\nflye_assembly_gfa"];
  4 --> 0e42ce51-c46b-45d8-baa4-45c0e98ac712;
  style 0e42ce51-c46b-45d8-baa4-45c0e98ac712 stroke:#2c3143,stroke-width:4px;
  3f297aed-7cee-4999-bbf4-69d84de6b64f["Output\nflye_assembly_info_tabular"];
  4 --> 3f297aed-7cee-4999-bbf4-69d84de6b64f;
  style 3f297aed-7cee-4999-bbf4-69d84de6b64f stroke:#2c3143,stroke-width:4px;
  5["Parse parameter value"];
  3 -->|list_output_txt| 5;
  3608e170-c462-42a2-8003-f3f65baa3834["Output\nparsed_extracted_samples_IDs_to_text"];
  5 --> 3608e170-c462-42a2-8003-f3f65baa3834;
  style 3608e170-c462-42a2-8003-f3f65baa3834 stroke:#2c3143,stroke-width:4px;
  6["medaka consensus pipeline"];
  4 -->|consensus| 6;
  0 -->|output| 6;
  9e5ad6ec-b408-4132-ba07-dec9fa626923["Output\nmedaka_gaps_in_draft_bed_file"];
  6 --> 9e5ad6ec-b408-4132-ba07-dec9fa626923;
  style 9e5ad6ec-b408-4132-ba07-dec9fa626923 stroke:#2c3143,stroke-width:4px;
  fcbd3e3f-2e93-4798-b696-dad7db9f2efd["Output\nmedaka_log_file"];
  6 --> fcbd3e3f-2e93-4798-b696-dad7db9f2efd;
  style fcbd3e3f-2e93-4798-b696-dad7db9f2efd stroke:#2c3143,stroke-width:4px;
  60656aac-ad2a-4c9b-9a68-b9fb18ae5595["Output\nmedaka_propability_h5_file"];
  6 --> 60656aac-ad2a-4c9b-9a68-b9fb18ae5595;
  style 60656aac-ad2a-4c9b-9a68-b9fb18ae5595 stroke:#2c3143,stroke-width:4px;
  c790d434-8e78-4df0-a0d4-8f9da0692158["Output\nmedaka_calls_of_draft_bam_file"];
  6 --> c790d434-8e78-4df0-a0d4-8f9da0692158;
  style c790d434-8e78-4df0-a0d4-8f9da0692158 stroke:#2c3143,stroke-width:4px;
  df361e19-b6d1-405b-96cc-b48c1ab7c604["Output\nsample_all_contigs"];
  6 --> df361e19-b6d1-405b-96cc-b48c1ab7c604;
  style df361e19-b6d1-405b-96cc-b48c1ab7c604 stroke:#2c3143,stroke-width:4px;
  7["Bandage Image"];
  4 -->|assembly_gfa| 7;
  9612a851-1f94-4d54-b001-5d082bcc9055["Output\nbandage_assembly_graph_image"];
  7 --> 9612a851-1f94-4d54-b001-5d082bcc9055;
  style 9612a851-1f94-4d54-b001-5d082bcc9055 stroke:#2c3143,stroke-width:4px;
  8["Compose text parameter value"];
  5 -->|text_param| 8;
  9["FASTA-to-Tabular"];
  6 -->|out_consensus| 9;
  de06c362-5b0a-4c29-956e-fbf02539789a["Output\nsample_specific_contigs_tabular_file_preparation"];
  9 --> de06c362-5b0a-4c29-956e-fbf02539789a;
  style de06c362-5b0a-4c29-956e-fbf02539789a stroke:#2c3143,stroke-width:4px;
  10["ABRicate"];
  6 -->|out_consensus| 10;
  8f227fc7-2d92-4c6f-af64-e841c1315b4f["Output\nabricate_with_vfdb_to_identify_genes_with_VFs"];
  10 --> 8f227fc7-2d92-4c6f-af64-e841c1315b4f;
  style 8f227fc7-2d92-4c6f-af64-e841c1315b4f stroke:#2c3143,stroke-width:4px;
  11["ABRicate"];
  6 -->|out_consensus| 11;
  fa021d98-d885-4834-ac62-f30d5792260e["Output\nabricate_report_using_ncbi_database_to_indentify_amr"];
  11 --> fa021d98-d885-4834-ac62-f30d5792260e;
  style fa021d98-d885-4834-ac62-f30d5792260e stroke:#2c3143,stroke-width:4px;
  12["Replace"];
  8 -->|out1| 12;
  9 -->|output| 12;
  174cb2c3-ed28-453c-8afb-85150e0b51ad["Output\nsample_specific_contigs_tabular_file"];
  12 --> 174cb2c3-ed28-453c-8afb-85150e0b51ad;
  style 174cb2c3-ed28-453c-8afb-85150e0b51ad stroke:#2c3143,stroke-width:4px;
  13["Replace"];
  8 -->|out1| 13;
  10 -->|report| 13;
  19e56e00-6eef-4a4e-9cc6-d93dbf9420ad["Output\nvfs"];
  13 --> 19e56e00-6eef-4a4e-9cc6-d93dbf9420ad;
  style 19e56e00-6eef-4a4e-9cc6-d93dbf9420ad stroke:#2c3143,stroke-width:4px;
  14["Replace"];
  8 -->|out1| 14;
  11 -->|report| 14;
  a8eb74a5-362b-4f0f-a944-672e27981a41["Output\namrs"];
  14 --> a8eb74a5-362b-4f0f-a944-672e27981a41;
  style a8eb74a5-362b-4f0f-a944-672e27981a41 stroke:#2c3143,stroke-width:4px;
  15["Tabular-to-FASTA"];
  12 -->|outfile| 15;
  a5bb1cbe-1bde-49a1-ad86-6d57b1319fbe["Output\ncontigs"];
  15 --> a5bb1cbe-1bde-49a1-ad86-6d57b1319fbe;
  style a5bb1cbe-1bde-49a1-ad86-6d57b1319fbe stroke:#2c3143,stroke-width:4px;
	
Nanopore Preprocessing
Bérénice Batut, Engy Nasr, Paul Zierep

Last updated Jun 7, 2024

Launch in Tutorial Mode question
License: MIT
Tests: ✅ Results: Not yet automated

flowchart TD
  0["ℹ️ Input Parameter\nsamples_profile"];
  style 0 fill:#ded,stroke:#393,stroke-width:4px;
  1["ℹ️ Input Collection\ncollection_of_all_samples"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Porechop"];
  1 -->|output| 2;
  34ea26db-11cb-41ee-85c3-75af8a53a2c0["Output\nporechop_output_trimmed_reads"];
  2 --> 34ea26db-11cb-41ee-85c3-75af8a53a2c0;
  style 34ea26db-11cb-41ee-85c3-75af8a53a2c0 stroke:#2c3143,stroke-width:4px;
  3["NanoPlot"];
  1 -->|output| 3;
  15ecf5b1-e0eb-405a-ac3a-359feb66d4cd["Output\nnanoplot_qc_on_reads_before_preprocessing_nanostats"];
  3 --> 15ecf5b1-e0eb-405a-ac3a-359feb66d4cd;
  style 15ecf5b1-e0eb-405a-ac3a-359feb66d4cd stroke:#2c3143,stroke-width:4px;
  304110f9-60d0-4ba2-8b3b-fae0e2a49554["Output\nnanoplot_on_reads_before_preprocessing_nanostats_post_filtering"];
  3 --> 304110f9-60d0-4ba2-8b3b-fae0e2a49554;
  style 304110f9-60d0-4ba2-8b3b-fae0e2a49554 stroke:#2c3143,stroke-width:4px;
  f2bd0a1f-cd60-4a36-a7d0-8025cc19ea2e["Output\nnanoplot_qc_on_reads_before_preprocessing_html_report"];
  3 --> f2bd0a1f-cd60-4a36-a7d0-8025cc19ea2e;
  style f2bd0a1f-cd60-4a36-a7d0-8025cc19ea2e stroke:#2c3143,stroke-width:4px;
  4["FastQC"];
  1 -->|output| 4;
  d0a64624-05d0-4068-835b-a025fc011760["Output\nfastqc_quality_check_before_preprocessing_html_file"];
  4 --> d0a64624-05d0-4068-835b-a025fc011760;
  style d0a64624-05d0-4068-835b-a025fc011760 stroke:#2c3143,stroke-width:4px;
  e61fef5d-1bc8-4c8e-be6a-f74e210e9920["Output\nfastqc_quality_check_before_preprocessing_text_file"];
  4 --> e61fef5d-1bc8-4c8e-be6a-f74e210e9920;
  style e61fef5d-1bc8-4c8e-be6a-f74e210e9920 stroke:#2c3143,stroke-width:4px;
  5["fastp"];
  2 -->|outfile| 5;
  a2219483-50b7-4aed-98dd-333ad2e12eb8["Output\nnanopore_sequenced_reads_processed_with_fastp_after_host_removal"];
  5 --> a2219483-50b7-4aed-98dd-333ad2e12eb8;
  style a2219483-50b7-4aed-98dd-333ad2e12eb8 stroke:#2c3143,stroke-width:4px;
  2a9a8b4d-458b-40e7-9a21-fb7108d5bbe4["Output\nnanopore_sequenced_reads_processed_with_fastp_after_host_removal_html_report"];
  5 --> 2a9a8b4d-458b-40e7-9a21-fb7108d5bbe4;
  style 2a9a8b4d-458b-40e7-9a21-fb7108d5bbe4 stroke:#2c3143,stroke-width:4px;
  6["MultiQC"];
  4 -->|text_file| 6;
  ebffe782-a56c-431f-8af4-c0cb8d7a02fc["Output\nmultiQC_stats_before_preprocessing"];
  6 --> ebffe782-a56c-431f-8af4-c0cb8d7a02fc;
  style ebffe782-a56c-431f-8af4-c0cb8d7a02fc stroke:#2c3143,stroke-width:4px;
  0f92196d-047d-4918-819d-c0ff7cd3ae85["Output\nmultiQC_html_report_before_preprocessing"];
  6 --> 0f92196d-047d-4918-819d-c0ff7cd3ae85;
  style 0f92196d-047d-4918-819d-c0ff7cd3ae85 stroke:#2c3143,stroke-width:4px;
  7["Map with minimap2"];
  0 -->|output| 7;
  5 -->|out1| 7;
  9d7bb3b7-09a1-401f-a132-bb35a53375ea["Output\nbam_map_to_host"];
  7 --> 9d7bb3b7-09a1-401f-a132-bb35a53375ea;
  style 9d7bb3b7-09a1-401f-a132-bb35a53375ea stroke:#2c3143,stroke-width:4px;
  8["NanoPlot"];
  5 -->|out1| 8;
  b5899290-4c57-4662-ad22-860654652ade["Output\nnanoplot_qc_on_reads_after_preprocessing_html_report"];
  8 --> b5899290-4c57-4662-ad22-860654652ade;
  style b5899290-4c57-4662-ad22-860654652ade stroke:#2c3143,stroke-width:4px;
  949bfdf5-3d79-4dad-bdd8-c3a25e6af4cf["Output\nnanoplot_on_reads_after_preprocessing_nanostats_post_filtering"];
  8 --> 949bfdf5-3d79-4dad-bdd8-c3a25e6af4cf;
  style 949bfdf5-3d79-4dad-bdd8-c3a25e6af4cf stroke:#2c3143,stroke-width:4px;
  42db7f93-919e-4bbb-81a1-06411a9da410["Output\nnanoplot_qc_on_reads_after_preprocessing_nanostats"];
  8 --> 42db7f93-919e-4bbb-81a1-06411a9da410;
  style 42db7f93-919e-4bbb-81a1-06411a9da410 stroke:#2c3143,stroke-width:4px;
  9["FastQC"];
  5 -->|out1| 9;
  09306471-afa0-4106-9cc7-259b93dfc862["Output\nfastqc_quality_check_after_preprocessing_text_file"];
  9 --> 09306471-afa0-4106-9cc7-259b93dfc862;
  style 09306471-afa0-4106-9cc7-259b93dfc862 stroke:#2c3143,stroke-width:4px;
  084f982f-20f1-457e-8012-91ebbb85633d["Output\nfastqc_quality_check_after_preprocessing_html_file"];
  9 --> 084f982f-20f1-457e-8012-91ebbb85633d;
  style 084f982f-20f1-457e-8012-91ebbb85633d stroke:#2c3143,stroke-width:4px;
  10["Split BAM by reads mapping status"];
  7 -->|alignment_output| 10;
  14a53fe2-f296-43aa-86b7-243278c1050c["Output\nnon_host_sequences_bam"];
  10 --> 14a53fe2-f296-43aa-86b7-243278c1050c;
  style 14a53fe2-f296-43aa-86b7-243278c1050c stroke:#2c3143,stroke-width:4px;
  3b1e626f-6bc1-484c-be01-366534361b73["Output\nhost_sequences_bam"];
  10 --> 3b1e626f-6bc1-484c-be01-366534361b73;
  style 3b1e626f-6bc1-484c-be01-366534361b73 stroke:#2c3143,stroke-width:4px;
  11["Select"];
  9 -->|text_file| 11;
  a809853b-119f-44d2-986b-8d2006439fbe["Output\ntotal_sequences_before_hosts_sequences_removal"];
  11 --> a809853b-119f-44d2-986b-8d2006439fbe;
  style a809853b-119f-44d2-986b-8d2006439fbe stroke:#2c3143,stroke-width:4px;
  12["Samtools fastx"];
  10 -->|mapped| 12;
  10d4eaec-81d8-444e-8075-7b77a1fb6870["Output\nhost_sequences_fastq"];
  12 --> 10d4eaec-81d8-444e-8075-7b77a1fb6870;
  style 10d4eaec-81d8-444e-8075-7b77a1fb6870 stroke:#2c3143,stroke-width:4px;
  13["Samtools fastx"];
  10 -->|unmapped| 13;
  0c2dd74d-ac4f-45cf-839c-50386a7ece28["Output\nnon_host_sequences_fastq"];
  13 --> 0c2dd74d-ac4f-45cf-839c-50386a7ece28;
  style 0c2dd74d-ac4f-45cf-839c-50386a7ece28 stroke:#2c3143,stroke-width:4px;
  14["Collapse Collection"];
  11 -->|out_file1| 14;
  15["Filter failed datasets"];
  12 -->|output| 15;
  16["Kraken2"];
  13 -->|output| 16;
  203d303e-8f3a-4242-971f-b345842ebdb8["Output\nkraken2_with_kalamri_database_output"];
  16 --> 203d303e-8f3a-4242-971f-b345842ebdb8;
  style 203d303e-8f3a-4242-971f-b345842ebdb8 stroke:#2c3143,stroke-width:4px;
  843afd4d-23a8-46e7-b945-8b67dd7ae341["Output\nkraken2_with_kalamri_database_report"];
  16 --> 843afd4d-23a8-46e7-b945-8b67dd7ae341;
  style 843afd4d-23a8-46e7-b945-8b67dd7ae341 stroke:#2c3143,stroke-width:4px;
  17["Cut"];
  14 -->|output| 17;
  d07be9f1-d250-4008-91ee-59a68521eb56["Output\nquality_retained_all_reads"];
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  18["FastQC"];
  15 -->|output| 18;
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  19["Krakentools: Extract Kraken Reads By ID"];
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  16 -->|report_output| 19;
  16 -->|output| 19;
  57e3b725-8e13-40b2-9acc-31fd56ebc80a["Output\ncollection_of_preprocessed_samples"];
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  20["Select"];
  18 -->|text_file| 20;
  3ba35c71-32f0-4741-98d4-ea8522e27500["Output\ntotal_sequences_after_hosts_sequences_removal"];
  20 --> 3ba35c71-32f0-4741-98d4-ea8522e27500;
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  21["Collapse Collection"];
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  22["Cut"];
  21 -->|output| 22;
  cef36c68-4549-4fd6-b7c8-71fb21df012f["Output\nquality_retained_hosts_reads"];
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  23["Column join"];
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  24["Compute"];
  23 -->|tabular_output| 24;
  25["Column Regex Find And Replace"];
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  26["MultiQC"];
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  13cbf6c7-6954-4458-aa66-a5b020c63822["Output\nmultiQC_stats_after_preprocessing"];
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Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation
Engy Nasr, Bérénice Batut, Paul Zierep

Last updated Jun 7, 2024

Launch in Tutorial Mode question
License: MIT
Tests: ❌ Results: Not yet automated

flowchart TD
  0["ℹ️ Input Collection\namr_identified_by_ncbi"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nvfs_of_genes_identified_by_vfdb"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nmetadata"];
  style 2 stroke:#2c3143,stroke-width:4px;
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  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nmapping_mean_depth_per_sample"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Collection\namrs"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["ℹ️ Input Dataset\nmapping_coverage_percentage_per_sample"];
  style 6 stroke:#2c3143,stroke-width:4px;
  7["ℹ️ Input Dataset\nnumber_of_variants_per_sample"];
  style 7 stroke:#2c3143,stroke-width:4px;
  8["ℹ️ Input Collection\ncontigs"];
  style 8 stroke:#2c3143,stroke-width:4px;
  9["ℹ️ Input Collection\nvfs"];
  style 9 stroke:#2c3143,stroke-width:4px;
  10["Filter failed datasets"];
  0 -->|output| 10;
  11["Filter failed datasets"];
  1 -->|output| 11;
  12["Bar chart"];
  3 -->|output| 12;
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  13["Bar chart"];
  3 -->|output| 13;
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  14["Bar chart"];
  4 -->|output| 14;
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  14 --> a71ebb67-1154-4f25-a62d-e8fa2b839e2e;
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  15["Filter failed datasets"];
  5 -->|output| 15;
  16["Bar chart"];
  6 -->|output| 16;
  2567360e-d39f-4316-84f5-77aaf8e8198c["Output\nmapping_coverage_percentage_per_sample_fig"];
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  17["Bar chart"];
  7 -->|output| 17;
  68c76f06-d2ea-4280-9e6f-a7b4f1568389["Output\nnumber_of_Variants_and_SNPs_indentified_fig"];
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  8 -->|output| 18;
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  9 -->|output| 19;
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  10 -->|output| 20;
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  11 -->|output| 21;
  22["Remove beginning"];
  15 -->|output| 22;
  23["Collapse Collection"];
  18 -->|output| 23;
  86910e39-57bf-4a76-ac4c-739340fd2387["Output\nall_samples_contigs_in_one_fasta_file"];
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  19 -->|output| 24;
  02b996c6-a912-4e4e-b3ec-49601faaa452["Output\nall_vfs_in_one_tabular"];
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  26["Count"];
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  27["Count"];
  21 -->|out_file1| 27;
  28["Group"];
  21 -->|out_file1| 28;
  29["Unique"];
  22 -->|out_file1| 29;
  30["Split by group"];
  24 -->|output| 30;
  59f8cb09-424b-47b1-b94b-a612c2610cab["Output\nsplit_by_group_collection"];
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  35["Cut"];
  29 -->|outfile| 35;
  36["Cut"];
  30 -->|split_output| 36;
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  42["Remove beginning"];
  36 -->|out_file1| 42;
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  44["Column Regex Find And Replace"];
  38 -->|output| 44;
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  39 -->|output| 45;
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  46["Column Regex Find And Replace"];
  40 -->|tabular_output| 46;
  f5c221e3-00ef-4834-9a5f-a94c97fd6764["Output\nheatmap_table"];
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  41 -->|output| 47;
  48["bedtools getfasta"];
  23 -->|output| 48;
  42 -->|out_file1| 48;
  82ce2107-89a3-438c-95bb-dc871b5258b7["Output\nfiltered_sequences_with_vfs_fasta"];
  48 --> 82ce2107-89a3-438c-95bb-dc871b5258b7;
  style 82ce2107-89a3-438c-95bb-dc871b5258b7 stroke:#2c3143,stroke-width:4px;
  49["Regex Find And Replace"];
  43 -->|output| 49;
  50["Multi-Join"];
  45 -->|out_file1| 50;
  44 -->|out_file1| 50;
  51["Heatmap w ggplot"];
  46 -->|out_file1| 51;
  c0417c91-a513-4c6a-9a62-3aac2f1f8e85["Output\nheatmap_pdf"];
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  style c0417c91-a513-4c6a-9a62-3aac2f1f8e85 stroke:#2c3143,stroke-width:4px;
  97816bc2-fd0c-4077-a721-8dd1470879d1["Output\nheatmap_png"];
  51 --> 97816bc2-fd0c-4077-a721-8dd1470879d1;
  style 97816bc2-fd0c-4077-a721-8dd1470879d1 stroke:#2c3143,stroke-width:4px;
  52["Filter empty datasets"];
  47 -->|out_file1| 52;
  53["ClustalW"];
  48 -->|output| 53;
  9b7bd78c-f112-480b-a7df-c10711af254c["Output\nclustalw_on_input_dnd"];
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  style 9b7bd78c-f112-480b-a7df-c10711af254c stroke:#2c3143,stroke-width:4px;
  6af20322-24da-4036-80de-37bed2d25848["Output\nclustalw_on_input_clustal"];
  53 --> 6af20322-24da-4036-80de-37bed2d25848;
  style 6af20322-24da-4036-80de-37bed2d25848 stroke:#2c3143,stroke-width:4px;
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  49 -->|out_file1| 54;
  55["Replace Text"];
  50 -->|outfile| 55;
  91745da0-0b8d-4a7a-b927-b36107f17ec5["Output\nvfs_amrs_count_table"];
  55 --> 91745da0-0b8d-4a7a-b927-b36107f17ec5;
  style 91745da0-0b8d-4a7a-b927-b36107f17ec5 stroke:#2c3143,stroke-width:4px;
  56["FASTA-to-Tabular"];
  52 -->|output| 56;
  57["Filter empty datasets"];
  53 -->|output| 57;
  32d00c1d-68c4-4069-8d5d-023aabdfadbe["Output\nfiltered_empty_datasets"];
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  58["FASTA-to-Tabular"];
  54 -->|output| 58;
  59["Cut"];
  56 -->|output| 59;
  60["FASTTREE"];
  57 -->|output| 60;
  aacdfe45-eb0c-4f6e-a479-eeb170774757["Output\nfasttree_nhx"];
  60 --> aacdfe45-eb0c-4f6e-a479-eeb170774757;
  style aacdfe45-eb0c-4f6e-a479-eeb170774757 stroke:#2c3143,stroke-width:4px;
  61["Cut"];
  58 -->|output| 61;
  62["Group"];
  59 -->|out_file1| 62;
  63["Newick Display"];
  60 -->|output| 63;
  0c22178c-dc85-4137-80e2-f3040b92bd20["Output\nnewick_genes_tree_graphs_collection"];
  63 --> 0c22178c-dc85-4137-80e2-f3040b92bd20;
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  65["Tabular-to-FASTA"];
  62 -->|out_file1| 65;
  66["Tabular-to-FASTA"];
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  65 -->|output| 67;
  68["FASTA Merge Files and Filter Unique Sequences"];
  66 -->|output| 68;
  69["ClustalW"];
  67 -->|output| 69;
  70["ClustalW"];
  68 -->|output| 70;
  71["FASTTREE"];
  69 -->|output| 71;
  72["FASTTREE"];
  70 -->|output| 72;
  73["Newick Display"];
  71 -->|output| 73;
  1f9cb2cf-219f-48de-8058-d6d45f3b3158["Output\nall_samples_phylogenetic_tree_based_amrs"];
  73 --> 1f9cb2cf-219f-48de-8058-d6d45f3b3158;
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  74["Newick Display"];
  72 -->|output| 74;
  6bb4b32b-7cca-4e04-8120-be9f64ccba39["Output\nall_samples_phylogenetic_tree_based_vfs"];
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Taxonomy Profiling and Visualization with Krona
Engy Nasr, Bérénice Batut, Paul Zierep

Last updated Jun 7, 2024

Launch in Tutorial Mode question
License: MIT
Tests: ✅ Results: Not yet automated

flowchart TD
  0["ℹ️ Input Collection\ncollection_of_preprocessed_samples"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Parameter\nkraken_database"];
  style 1 fill:#ded,stroke:#393,stroke-width:4px;
  2["Kraken2"];
  1 -->|output| 2;
  0 -->|output| 2;
  26f9041f-d8a4-4f64-8a53-404d5c7e2f61["Output\nkraken2_with_pluspf_database_output"];
  2 --> 26f9041f-d8a4-4f64-8a53-404d5c7e2f61;
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  f2ddd05b-66a0-4cea-9da6-ed107eecbe1b["Output\nkraken2_with_pluspf_database_output_report"];
  2 --> f2ddd05b-66a0-4cea-9da6-ed107eecbe1b;
  style f2ddd05b-66a0-4cea-9da6-ed107eecbe1b stroke:#2c3143,stroke-width:4px;
  3["Krakentools: Convert kraken report file"];
  2 -->|report_output| 3;
  c490ab8d-1b1d-4914-aa51-a62a967a4018["Output\nconverted_kraken_report"];
  3 --> c490ab8d-1b1d-4914-aa51-a62a967a4018;
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  4["Krona pie chart"];
  3 -->|output| 4;
  dcc857c6-f579-4c74-84ec-bb6ce3794a56["Output\nkrona_pie_chart"];
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Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands-on: Importing a workflow
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on galaxy-upload Import at the top-right of the screen
  • Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  • Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL