Nanopore Preprocessing

Run Workflow in Galaxy

• Galaxy France
• Galaxy Europe
• Galaxy Australia
• Galaxy Main
• Import to another server (≥23.0+ only!)

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;

Inputs

Outputs

Tools

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.

Importing into Galaxy

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:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/nanopore_preprocessing.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows