host-contamination-removal-long-reads/main
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Tests This workflow takes Nanopore fastq(.gz) files and runs Minimap2 to map the reads against a reference genome (human, by default). It filters the output to keep only the unmapped reads and generates mapping statistics that are aggregated into a MultiQC report.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Contaminant Reference Genome (long-reads) | #main/Host/Contaminant Reference Genome (long-reads) | Reads not mapping to this reference genome will be kept. |
|
| Long-reads | #main/Long-reads | Long-reads as a collection of fastqsanger(.gz) files |
|
| Profile of preset options for the mapping (long-read) | #main/Profile of preset options for the mapping (long-read) | Each profile comes with the preconfigured settings mentioned in parentheses. You can customize each profile further in the indexing, mapping and alignment options sections below. If you do not select a profile here, the tool will use the per-parameter defaults listed in the below sections unless you customize them. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | minimap2 | Map the reads against a reference genome and output the ones not mapping the reference genome toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy2 |
| 4 | QualiMap | Generation of mapping statistics toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0 |
| 5 | Split BAM | Split BAM into mapped and unmapped toolshed.g2.bx.psu.edu/repos/iuc/bamtools_split_mapped/bamtools_split_mapped/2.5.2+galaxy2 |
| 6 | Flatten collection | Prepare QualiMap stats for MultiQC __FLATTEN__ |
| 7 | Samtools fastx | Extractions of FastQ from the unmapped reads toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.22+galaxy1 |
| 8 | MultiQC | Aggregation of the mapping statistics for all samples toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| MultiQC HTML Report | #main/MultiQC HTML Report | n/a |
|
| QualiMap Statistics | #main/QualiMap Statistics | n/a |
|
| QualiMap mapping statistics | #main/QualiMap mapping statistics | n/a |
|
| Reads without Host or Contamination | #main/Reads without Host or Contamination | n/a |
|
Version History
v0.1 (earliest) Created 6th Dec 2025 at 03:02 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1a6dd049
Creators and SubmitterViews: 1023 Downloads: 3693 Runs: 1
Created: 6th Dec 2025 at 03:02
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https://orcid.org/0000-0001-9852-1987
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