host-contamination-removal-short-reads/main
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Tests This workflow takes paired-end Illumina fastq(.gz) files and runs Bowtie to map the reads against a reference genome (human, by default) and keep only the reads that do not align. MultiQC is used to aggregate the mapping reports.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Choose Reference Genome | Choose Reference Genome | Choose a reference genome from a built in list or from the history |
|
| Contaminant Reference Genome | Host/Contaminant Reference Genome | Reads not mapping to this reference genome will be kept |
|
| Reference genome file | Reference genome file | Select a reference genome from the history |
|
| Short-reads | Short-reads | Short-reads as a paired-end collection of fastqsanger(.gz) files |
|
Steps
| ID | Name | Description |
|---|---|---|
| 4 | Map parameter value | toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0 |
| 5 | Map parameter value | toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0 |
| 6 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 7 | Bowtie2-map reads against a built in reference genome | Map the reads against a reference genome and output the ones not mapping the reference genome toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.4+galaxy0 |
| 8 | Bowtie2-map reads against a reference genome in the history | Map the reads against a reference genome and output the ones not mapping the reference genome toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.4+galaxy0 |
| 9 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 10 | 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 |
|---|---|---|---|
| Contamination Filtered Reads from Local Index | Contamination Filtered Reads from Local Index | n/a |
|
| Bowtie2 Mapping Statistics from Local Index | Bowtie2 Mapping Statistics from Local Index | n/a |
|
| Contamination Filtered Reads from Reference Input | Contamination Filtered Reads from Reference Input | n/a |
|
| Bowtie2 Mapping Statistics from Reference Input | Bowtie2 Mapping Statistics from Reference Input | n/a |
|
| MultiQC HTML Report | MultiQC HTML Report | n/a |
|
Version History
v0.1 (earliest) Created 6th Dec 2025 at 03:02 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.125561f7
Creators and SubmitterViews: 1560 Downloads: 6178 Runs: 2
Created: 6th Dec 2025 at 03:01
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https://orcid.org/0000-0001-9852-1987
Teams: Intergalactic Workflow Commission (IWC), Vertebrate Genomes Pipelines in Galaxy, nf-core
Organizations: Bots, European Galaxy Team
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