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Update EU wf hyperlinks #302

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Update EU wf hyperlinks #302

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10 changes: 5 additions & 5 deletions genomics/global_platform/README.md
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Expand Up @@ -52,11 +52,11 @@ Workflow description. Clicking <kbd>US</kbd>, <kbd>EU</kbd>, or <kbd>AU</kbd> bu

| Workflow | Input data | Read aligner | Variant caller |
|----------|-------------|---|---|---|
|1. Illumina RNAseq SE<br>[<kbd>EU</kbd>](https://usegalaxy.eu/u/wolfgang-maier/w/covid-19-variation-analysis-on-se-data)[<kbd>US</kbd>](https://usegalaxy.org/u/aun1/w/covid-19-variation-analysis-on-wgs-se-data)[<kbd>AU</kbd>](https://usegalaxy.org.au/u/nekrut/w/covid-19-variation-analysis-on-wgs-se-data) | Single end data derived from RNAseq experiments | `bowtie2` | `lofreq` |
|2. Illumina RNAseq PE<br>[<kbd>EU</kbd>](https://usegalaxy.eu/u/wolfgang-maier/w/covid-19-variation-analysis-on-pe-data)[<kbd>US</kbd>](https://usegalaxy.org/u/aun1/w/covid-19-variation-analysis-on-wgs-pe-data)[<kbd>AU</kbd>](https://usegalaxy.org.au/u/nekrut/w/covid-19-variation-analysis-on-wgs-pe-data) | Paired end data derived from RNAseq experiments | `bwa-mem` | `lofreq` |
|3. Illumina ARTIC<br>[<kbd>EU</kbd>](https://usegalaxy.eu/u/wolfgang-maier/w/covid19-variation-analysis-on-artic-pe)[<kbd>US</kbd>](https://usegalaxy.org/u/aun1/w/covid-19-variation-analysis-on-artic-pe-data-1)[<kbd>AU</kbd>](https://usegalaxy.org.au/u/nekrut/w/covid-19-variation-analysis-on-artic-pe-data) | Paired-end data generated with ARTIC protocols | `bwa-mem` | `lofreq` |
|4. ONT ARTIC<br>[<kbd>EU</kbd>](https://usegalaxy.eu/u/wolfgang-maier/w/covid-19-variation-analysis-of-artic-ont-data)[<kbd>US</kbd>](https://usegalaxy.org/u/aun1/w/covid-19-variation-analysis-of-artic-ont-data)[<kbd>AU</kbd>](https://usegalaxy.org.au/u/nekrut/w/covid-19-variation-analysis-of-artic-ont-data ) | ONT fastq files generated with ARTIC protocols | `minimap2` | `medaka` |
|5. Reporting<br>[<kbd>EU</kbd>](https://usegalaxy.eu/u/wolfgang-maier/w/covid19-variation-analysis-reporting)[<kbd>US</kbd>](https://usegalaxy.org/u/aun1/w/covid-19-variation-analysis-reporting)[<kbd>AU</kbd>](https://usegalaxy.org.au/u/nekrut/w/covid-19-variation-analysis-reporting)| Output of any of the above workflows | - | - |
|1. Illumina RNAseq SE<br>[<kbd>EU</kbd>](https://usegalaxy.eu/u/sars-cov2-bot/w/covid-19-variation-analysis-on-wgs-se-data---iwc-version-012)[<kbd>US</kbd>](https://usegalaxy.org/u/aun1/w/covid-19-variation-analysis-on-wgs-se-data)[<kbd>AU</kbd>](https://usegalaxy.org.au/u/nekrut/w/covid-19-variation-analysis-on-wgs-se-data) | Single end data derived from RNAseq experiments | `bowtie2` | `lofreq` |
|2. Illumina RNAseq PE<br>[<kbd>EU</kbd>](https://usegalaxy.eu/u/sars-cov2-bot/w/covid-19-variation-analysis-on-wgs-pe-data-imported-from-uploaded-file)[<kbd>US</kbd>](https://usegalaxy.org/u/aun1/w/covid-19-variation-analysis-on-wgs-pe-data)[<kbd>AU</kbd>](https://usegalaxy.org.au/u/nekrut/w/covid-19-variation-analysis-on-wgs-pe-data) | Paired end data derived from RNAseq experiments | `bwa-mem` | `lofreq` |
|3. Illumina ARTIC<br>[<kbd>EU</kbd>](https://usegalaxy.eu/u/sars-cov2-bot/w/covid-19-variation-analysis-on-artic-pe-data-3)[<kbd>US</kbd>](https://usegalaxy.org/u/aun1/w/covid-19-variation-analysis-on-artic-pe-data-1)[<kbd>AU</kbd>](https://usegalaxy.org.au/u/nekrut/w/covid-19-variation-analysis-on-artic-pe-data) | Paired-end data generated with ARTIC protocols | `bwa-mem` | `lofreq` |
|4. ONT ARTIC<br>[<kbd>EU</kbd>](https://usegalaxy.eu/u/sars-cov2-bot/w/covid-19-variation-analysis-of-artic-ont-data---iwc-version-03)[<kbd>US</kbd>](https://usegalaxy.org/u/aun1/w/covid-19-variation-analysis-of-artic-ont-data)[<kbd>AU</kbd>](https://usegalaxy.org.au/u/nekrut/w/covid-19-variation-analysis-of-artic-ont-data ) | ONT fastq files generated with ARTIC protocols | `minimap2` | `medaka` |
|5. Reporting<br>[<kbd>EU</kbd>](https://usegalaxy.eu/u/sars-cov2-bot/w/imported-covid-19-variation-analysis-reporting)[<kbd>US</kbd>](https://usegalaxy.org/u/aun1/w/covid-19-variation-analysis-reporting)[<kbd>AU</kbd>](https://usegalaxy.org.au/u/nekrut/w/covid-19-variation-analysis-reporting)| Output of any of the above workflows | - | - |

## Application of workflows for analysis of intrahost variation

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