bacterial-quality-and-contamination-control-post-assembly/main
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This workflow performs quality and contamination control analysis on assembled contigs to assess bacterial genome quality and taxonomic assignment
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Fasta boolean | #main/Fasta boolean | True if fasta metaWF False if fastq metaWF |
|
| Fastq boolean | #main/Fastq boolean | True if fastq metaWF False if fasta metaWF |
|
| Input sequence contigs FASTA | #main/Input sequence contigs FASTA | Fasta as contigs from raw reads assembly. |
|
| Input sequence reads (forward) | #main/Input sequence reads (forward) | Should be the forward strand of the paired end reads. |
|
| Input sequence reads (reverse) | #main/Input sequence reads (reverse) | Should be the reverse strand of the paired end reads. |
|
| Select a taxonomy database | #main/Select a taxonomy database | Select the database to use for assigning taxonomies for Kraken2 and Bracken. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 6 | Pick R1 reads with fastq | When the fastq metaWF is used, the R1 trimmed file is selected toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 7 | Pick R2 reads with fastq | When the fastq metaWF is used, the R2 trimmed file is selected toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 8 | Quast quality fasta | quast_quality_fasta toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy0 |
| 9 | Checkm2 quality | Checkm2 to predict the completeness and contamination in an assembly toolshed.g2.bx.psu.edu/repos/iuc/checkm2/checkm2/1.0.2+galaxy1 |
| 10 | Kraken taxonomy assignation | kraken_taxonomy_assignation toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy1 |
| 11 | Quast quality fastq | quast_quality_fastq toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy0 |
| 12 | Collapse checkm2 protein collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 13 | Collapse checkm2 diamond collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 14 | Bracken abundance estimation | bracken_abundance_estimation toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.1+galaxy0 |
| 15 | Pick generate tabular quast report | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 16 | Pick generate html quast report | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 17 | ToolDistillator | ToolDistillator extracts results from tools and creates a JSON file for each tool toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.4+galaxy0 |
| 18 | ToolDistillator summarize | ToolDistillator summarize groups all JSON file into a unique JSON file toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.4+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Bracken Kraken tabular report | #main/Bracken Kraken tabular report | n/a |
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| Bracken tabular report | #main/Bracken tabular report | n/a |
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| Checkm2 diamond files | #main/Checkm2 diamond files | n/a |
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| Checkm2 protein files | #main/Checkm2 protein files | n/a |
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| Checkm2 tabular report | #main/Checkm2 tabular report | n/a |
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| Kraken2 sequence assignation | #main/Kraken2 sequence assignation | n/a |
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| Kraken2 tabular report | #main/Kraken2 tabular report | n/a |
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| QUAST tabular report for FASTQ files | #main/QUAST tabular report for FASTQ files | n/a |
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| Quast HTMl report for FASTA files | #main/Quast HTMl report for FASTA files | n/a |
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| Quast HTMl report for FASTQ files | #main/Quast HTMl report for FASTQ files | n/a |
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| Quast tabular report for FASTA files | #main/Quast tabular report for FASTA files | n/a |
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| Tooldistillator results control | #main/Tooldistillator results control | n/a |
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| Tooldistillator summarize control | #main/Tooldistillator summarize control | n/a |
|
Version History
v1.0.2 (latest) Created 4th Dec 2025 at 03:02 by WorkflowHub Bot
Updated to v1.0.2
Frozen
v1.0.27729946
v1.0 (earliest) Created 22nd Aug 2025 at 03:02 by WorkflowHub Bot
Updated to v1.0
Frozen
v1.0
0174a64
Creators and Submitter
Activity
Views: 1974 Downloads: 14930 Runs: 0
Created: 22nd Aug 2025 at 03:02
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Teams: Intergalactic Workflow Commission (IWC), Vertebrate Genomes Pipelines in Galaxy, nf-core
Organizations: Bots, European Galaxy Team
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