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| Main Authors: | , , , , , , , , |
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| Formato: | Recurso digital |
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Zenodo
2025
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| Acesso em linha: | https://doi.org/10.5281/zenodo.16759358 |
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Sumário:
- <h3>Summary of changes</h3> <ul> <li>filtering is set now by default</li> <li>defaults reflect best settings from benchmarking human decontamination</li> <li>improvements to memory and time requirements</li> </ul> <h3>Detailed changes</h3> <h3><code>Added</code></h3> <ul> <li><a href="https://github.com/nf-core/detaxizer/pull/70">PR #70</a> - Filtering is now default, <code>--skip_filter</code> was added (by @d4straub)</li> <li><a href="https://github.com/nf-core/detaxizer/pull/71">PR #71</a> - Add usage information learned from our benchmarking (by @d4straub)</li> </ul> <h3><code>Changed</code></h3> <ul> <li><a href="https://github.com/nf-core/detaxizer/pull/65">PR #65</a>,<a href="https://github.com/nf-core/detaxizer/pull/69">PR #69</a> - Template update for nf-core/tools 3.3.2 (by @d4straub)</li> <li><a href="https://github.com/nf-core/detaxizer/pull/72">PR #72</a> - Default for <code>--kraken2db</code> was changed from 'https://genome-idx.s3.amazonaws.com/kraken/k2_standard_08gb_20240904.tar.gz' to 'https://genome-idx.s3.amazonaws.com/kraken/k2_standard_20240605.tar.gz'. That database is much larger (60GB) but default settings will therefore reflect best decontamination performance in benchmarks (by @d4straub)</li> <li><a href="https://github.com/nf-core/detaxizer/pull/73">PR #73</a> - Doubled memory allocation for ISOLATE_BBDUK_IDS (by @d4straub)</li> <li><a href="https://github.com/nf-core/detaxizer/pull/75">PR #75</a> - Updated version and contributors (by @d4straub)</li> </ul> <h3><code>Fixed</code></h3> <ul> <li><a href="https://github.com/nf-core/detaxizer/pull/62">PR #62</a> - Use dnaio to reduce memory spikes during renaming (by @bede)</li> <li><a href="https://github.com/nf-core/detaxizer/pull/77">PR #77</a> - Fixed conda versions to exactly follow container versions (by @d4straub)</li> <li><a href="https://github.com/nf-core/detaxizer/pull/78">PR #78</a> - Update typos, re-add code comments (by @d4straub)</li> </ul> <h3><code>Dependencies</code></h3> <p>| Software | Previous version | New version | | -------- | ---------------- | ----------- | | MultiQC | 1.27 | 1.29 | | tar | 1.3 | 1.34 |</p> <h3><code>Removed</code></h3> <ul> <li><a href="https://github.com/nf-core/detaxizer/pull/70">PR #70</a> - Filtering is now default, <code>--enable_filter</code> was removed and replaced by <code>--skip_filter</code> (by @d4straub)</li> </ul>