| _version_ | 1866902339971973120 |
|---|---|
| author | Chris Wright Chris Alder Sarah Griffiths Matthew Parker Julian Libiseller-Egger Sam Nicholls Georgette Tanner Natalia Garcia Garcia Neil Horner Pablo Gonzalez Sirisha Hesketh nanofriend |
| author_facet | Chris Wright Chris Alder Sarah Griffiths Matthew Parker Julian Libiseller-Egger Sam Nicholls Georgette Tanner Natalia Garcia Garcia Neil Horner Pablo Gonzalez Sirisha Hesketh nanofriend |
| contents | <h3>Added</h3> <ul> <li>Workflow now accepts BAM as well as FASTQ files as input (using the <code>--bam</code> or <code>--fastq</code> parameters, respectively)</li> <li><code>--override_basecaller_cfg</code> parameter for cases where automatic basecall model detection fails or users wish to override the automatic choice.</li> </ul> <h3>Removed</h3> <ul> <li>The <code>--basecaller_cfg</code>, <code>--medaka_consensus_model</code>, and <code>--medaka_variant_model</code> parameters as the appropriate Medaka model is now automatically determined from the input data.</li> </ul> <h3>Changed</h3> <ul> <li>New docker images for <a href="https://hub.docker.com/r/ontresearch/resfinder">resfinder</a> and <a href="https://hub.docker.com/r/ontresearch/mlst">mlst</a>.</li> <li>Updated Medaka to v1.12.0.</li> <li>Updated minimum computer specs as flye was not performing robustly.</li> </ul> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_16758970 |
| institution | Zenodo |
| language | |
| publishDate | 2024 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | epi2me-labs/wf-bacterial-genomes: v1.3.0 Chris Wright Chris Alder Sarah Griffiths Matthew Parker Julian Libiseller-Egger Sam Nicholls Georgette Tanner Natalia Garcia Garcia Neil Horner Pablo Gonzalez Sirisha Hesketh nanofriend <h3>Added</h3> <ul> <li>Workflow now accepts BAM as well as FASTQ files as input (using the <code>--bam</code> or <code>--fastq</code> parameters, respectively)</li> <li><code>--override_basecaller_cfg</code> parameter for cases where automatic basecall model detection fails or users wish to override the automatic choice.</li> </ul> <h3>Removed</h3> <ul> <li>The <code>--basecaller_cfg</code>, <code>--medaka_consensus_model</code>, and <code>--medaka_variant_model</code> parameters as the appropriate Medaka model is now automatically determined from the input data.</li> </ul> <h3>Changed</h3> <ul> <li>New docker images for <a href="https://hub.docker.com/r/ontresearch/resfinder">resfinder</a> and <a href="https://hub.docker.com/r/ontresearch/mlst">mlst</a>.</li> <li>Updated Medaka to v1.12.0.</li> <li>Updated minimum computer specs as flye was not performing robustly.</li> </ul> |
| title | epi2me-labs/wf-bacterial-genomes: v1.3.0 |
| url | https://doi.org/10.5281/zenodo.16758970 |