Workflow Type: Galaxy
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The workflow takes a HiFi reads collection, runs FastQC and SeqKit, filters with Cutadapt, and creates a MultiQC report. The main outputs are a collection of filtred reads, a report with raw and filtered reads stats, and a table with raw reads stats.
Inputs
ID | Name | Description | Type |
---|---|---|---|
HiFi raw reads collection | #main/HiFi raw reads collection | n/a |
|
Steps
ID | Name | Description |
---|---|---|
1 | FastQC HiFi raw | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 |
2 | Cutadapt | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 |
3 | SeqKit HiFi raw | toolshed.g2.bx.psu.edu/repos/iuc/seqkit_stats/seqkit_stats/2.8.1+galaxy0 |
4 | MultiQC HiFi | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0 |
5 | SeqKit HiFi | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
HiFi trimmed collection | #main/HiFi trimmed collection | n/a |
|
SeqKit HiFi raw table | #main/SeqKit HiFi raw table | n/a |
|
Version History
Version 2 (latest) Created 18th Sep 2024 at 14:14 by Diego De Panis
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Version 1 (earliest) Created 6th Oct 2023 at 14:17 by Diego De Panis
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ERGA
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Views: 3064 Downloads: 214 Runs: 34
Created: 6th Oct 2023 at 14:17
Last updated: 18th Sep 2024 at 14:15
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