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
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
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
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"]; 17 --> d07be9f1-d250-4008-91ee-59a68521eb56; style d07be9f1-d250-4008-91ee-59a68521eb56 stroke:#2c3143,stroke-width:4px; 18["FastQC"]; 15 -->|output| 18; b0ee6e31-0eb1-437d-8c04-fc3640b9a0b7["Output\nhosts_qc_text_file"]; 18 --> b0ee6e31-0eb1-437d-8c04-fc3640b9a0b7; style b0ee6e31-0eb1-437d-8c04-fc3640b9a0b7 stroke:#2c3143,stroke-width:4px; b72ff57b-0921-43bf-a817-6cd444c8f3cb["Output\nhosts_qc_html"]; 18 --> b72ff57b-0921-43bf-a817-6cd444c8f3cb; style b72ff57b-0921-43bf-a817-6cd444c8f3cb stroke:#2c3143,stroke-width:4px; 19["Krakentools: Extract Kraken Reads By ID"]; 5 -->|out1| 19; 16 -->|report_output| 19; 16 -->|output| 19; 57e3b725-8e13-40b2-9acc-31fd56ebc80a["Output\ncollection_of_preprocessed_samples"]; 19 --> 57e3b725-8e13-40b2-9acc-31fd56ebc80a; style 57e3b725-8e13-40b2-9acc-31fd56ebc80a stroke:#2c3143,stroke-width:4px; 20["Select"]; 18 -->|text_file| 20; 3ba35c71-32f0-4741-98d4-ea8522e27500["Output\ntotal_sequences_after_hosts_sequences_removal"]; 20 --> 3ba35c71-32f0-4741-98d4-ea8522e27500; style 3ba35c71-32f0-4741-98d4-ea8522e27500 stroke:#2c3143,stroke-width:4px; 21["Collapse Collection"]; 20 -->|out_file1| 21; 22["Cut"]; 21 -->|output| 22; cef36c68-4549-4fd6-b7c8-71fb21df012f["Output\nquality_retained_hosts_reads"]; 22 --> cef36c68-4549-4fd6-b7c8-71fb21df012f; style cef36c68-4549-4fd6-b7c8-71fb21df012f stroke:#2c3143,stroke-width:4px; 23["Column join"]; 17 -->|out_file1| 23; 22 -->|out_file1| 23; 24["Compute"]; 23 -->|tabular_output| 24; 25["Column Regex Find And Replace"]; 24 -->|out_file1| 25; 470892ee-dab9-48d7-ad97-45dbd52afaa7["Output\nremoved_hosts_percentage_tabular"]; 25 --> 470892ee-dab9-48d7-ad97-45dbd52afaa7; style 470892ee-dab9-48d7-ad97-45dbd52afaa7 stroke:#2c3143,stroke-width:4px; 26["MultiQC"]; 9 -->|text_file| 26; 25 -->|out_file1| 26; 0b1b5a73-36ee-42a2-a220-1ced6ec7378b["Output\nmultiQC_html_report_after_preprocessing"]; 26 --> 0b1b5a73-36ee-42a2-a220-1ced6ec7378b; style 0b1b5a73-36ee-42a2-a220-1ced6ec7378b stroke:#2c3143,stroke-width:4px; 13cbf6c7-6954-4458-aa66-a5b020c63822["Output\nmultiQC_stats_after_preprocessing"]; 26 --> 13cbf6c7-6954-4458-aa66-a5b020c63822; style 13cbf6c7-6954-4458-aa66-a5b020c63822 stroke:#2c3143,stroke-width:4px;
Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation
Engy Nasr, Bérénice Batut, Paul Zierep
Last updated Jun 7, 2024
Launch in Tutorial Mode
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; 3["ℹ️ Input Dataset\nremoved_hosts_percentage_tabular"]; 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; 0961166e-38b6-44e3-93db-100d821b0070["Output\nnumber_of_reads_before_host_removal_and_number_of_host_reads_found_per_sample_fig"]; 12 --> 0961166e-38b6-44e3-93db-100d821b0070; style 0961166e-38b6-44e3-93db-100d821b0070 stroke:#2c3143,stroke-width:4px; 13["Bar chart"]; 3 -->|output| 13; 548975e5-4619-49fc-9e95-4d7f4d761dfd["Output\nremoved_host_percentage_fig"]; 13 --> 548975e5-4619-49fc-9e95-4d7f4d761dfd; style 548975e5-4619-49fc-9e95-4d7f4d761dfd stroke:#2c3143,stroke-width:4px; 14["Bar chart"]; 4 -->|output| 14; a71ebb67-1154-4f25-a62d-e8fa2b839e2e["Output\nmapping_mean_depth_per_sample_fig"]; 14 --> a71ebb67-1154-4f25-a62d-e8fa2b839e2e; style a71ebb67-1154-4f25-a62d-e8fa2b839e2e stroke:#2c3143,stroke-width:4px; 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"]; 16 --> 2567360e-d39f-4316-84f5-77aaf8e8198c; style 2567360e-d39f-4316-84f5-77aaf8e8198c stroke:#2c3143,stroke-width:4px; 17["Bar chart"]; 7 -->|output| 17; 68c76f06-d2ea-4280-9e6f-a7b4f1568389["Output\nnumber_of_Variants_and_SNPs_indentified_fig"]; 17 --> 68c76f06-d2ea-4280-9e6f-a7b4f1568389; style 68c76f06-d2ea-4280-9e6f-a7b4f1568389 stroke:#2c3143,stroke-width:4px; 18["Filter failed datasets"]; 8 -->|output| 18; 19["Filter failed datasets"]; 9 -->|output| 19; 20["Remove beginning"]; 10 -->|output| 20; 21["Remove beginning"]; 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"]; 23 --> 86910e39-57bf-4a76-ac4c-739340fd2387; style 86910e39-57bf-4a76-ac4c-739340fd2387 stroke:#2c3143,stroke-width:4px; 24["Collapse Collection"]; 19 -->|output| 24; 02b996c6-a912-4e4e-b3ec-49601faaa452["Output\nall_vfs_in_one_tabular"]; 24 --> 02b996c6-a912-4e4e-b3ec-49601faaa452; style 02b996c6-a912-4e4e-b3ec-49601faaa452 stroke:#2c3143,stroke-width:4px; 25["Remove beginning"]; 19 -->|output| 25; 26["Count"]; 20 -->|out_file1| 26; 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"]; 30 --> 59f8cb09-424b-47b1-b94b-a612c2610cab; style 59f8cb09-424b-47b1-b94b-a612c2610cab stroke:#2c3143,stroke-width:4px; 31["Unique"]; 25 -->|out_file1| 31; 32["Cut"]; 26 -->|out_file1| 32; 33["Cut"]; 27 -->|out_file1| 33; 34["Filter empty datasets"]; 28 -->|out_file1| 34; 35["Cut"]; 29 -->|outfile| 35; 36["Cut"]; 30 -->|split_output| 36; eeb25a51-ea21-4a19-a196-55d5bd919b10["Output\nadjusted_abricate_vfs_tabular_part1"]; 36 --> eeb25a51-ea21-4a19-a196-55d5bd919b10; style eeb25a51-ea21-4a19-a196-55d5bd919b10 stroke:#2c3143,stroke-width:4px; 37["Cut"]; 31 -->|outfile| 37; 38["Collapse Collection"]; 32 -->|out_file1| 38; 39["Collapse Collection"]; 33 -->|out_file1| 39; 40["Column join"]; 34 -->|output| 40; 41["bedtools getfasta"]; 23 -->|output| 41; 35 -->|out_file1| 41; 42["Remove beginning"]; 36 -->|out_file1| 42; aaaa4446-0817-4e5c-aa1b-9ec384f2a363["Output\nadjusted_abricate_vfs_tabular_part2"]; 42 --> aaaa4446-0817-4e5c-aa1b-9ec384f2a363; style aaaa4446-0817-4e5c-aa1b-9ec384f2a363 stroke:#2c3143,stroke-width:4px; 43["bedtools getfasta"]; 23 -->|output| 43; 37 -->|out_file1| 43; 44["Column Regex Find And Replace"]; 38 -->|output| 44; 4809c36b-31ef-4664-8e4e-47f0f72152de["Output\namrs_count"]; 44 --> 4809c36b-31ef-4664-8e4e-47f0f72152de; style 4809c36b-31ef-4664-8e4e-47f0f72152de stroke:#2c3143,stroke-width:4px; 45["Column Regex Find And Replace"]; 39 -->|output| 45; 87efc81d-4d84-4af3-831f-dfe033c59f78["Output\nvfs_count"]; 45 --> 87efc81d-4d84-4af3-831f-dfe033c59f78; style 87efc81d-4d84-4af3-831f-dfe033c59f78 stroke:#2c3143,stroke-width:4px; 46["Column Regex Find And Replace"]; 40 -->|tabular_output| 46; f5c221e3-00ef-4834-9a5f-a94c97fd6764["Output\nheatmap_table"]; 46 --> f5c221e3-00ef-4834-9a5f-a94c97fd6764; style f5c221e3-00ef-4834-9a5f-a94c97fd6764 stroke:#2c3143,stroke-width:4px; 47["Regex Find And Replace"]; 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"]; 51 --> c0417c91-a513-4c6a-9a62-3aac2f1f8e85; 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"]; 53 --> 9b7bd78c-f112-480b-a7df-c10711af254c; 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; 54["Filter empty datasets"]; 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"]; 57 --> 32d00c1d-68c4-4069-8d5d-023aabdfadbe; style 32d00c1d-68c4-4069-8d5d-023aabdfadbe stroke:#2c3143,stroke-width:4px; 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; style 0c22178c-dc85-4137-80e2-f3040b92bd20 stroke:#2c3143,stroke-width:4px; 64["Group"]; 61 -->|out_file1| 64; 65["Tabular-to-FASTA"]; 62 -->|out_file1| 65; 66["Tabular-to-FASTA"]; 64 -->|out_file1| 66; 67["FASTA Merge Files and Filter Unique Sequences"]; 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; style 1f9cb2cf-219f-48de-8058-d6d45f3b3158 stroke:#2c3143,stroke-width:4px; 74["Newick Display"]; 72 -->|output| 74; 6bb4b32b-7cca-4e04-8120-be9f64ccba39["Output\nall_samples_phylogenetic_tree_based_vfs"]; 74 --> 6bb4b32b-7cca-4e04-8120-be9f64ccba39; style 6bb4b32b-7cca-4e04-8120-be9f64ccba39 stroke:#2c3143,stroke-width:4px;
Taxonomy Profiling and Visualization with Krona
Engy Nasr, Bérénice Batut, Paul Zierep
Last updated Jun 7, 2024
Launch in Tutorial Mode
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; style 26f9041f-d8a4-4f64-8a53-404d5c7e2f61 stroke:#2c3143,stroke-width:4px; 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; style c490ab8d-1b1d-4914-aa51-a62a967a4018 stroke:#2c3143,stroke-width:4px; 4["Krona pie chart"]; 3 -->|output| 4; dcc857c6-f579-4c74-84ec-bb6ce3794a56["Output\nkrona_pie_chart"]; 4 --> dcc857c6-f579-4c74-84ec-bb6ce3794a56; style dcc857c6-f579-4c74-84ec-bb6ce3794a56 stroke:#2c3143,stroke-width:4px;
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