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Recent Releases of miassembler

miassembler - Bump memory for the Phyx reads decontamination

What's Changed

  • Increase PhiX read decontamination memory by @jmattock5 in https://github.com/EBI-Metagenomics/miassembler/pull/54
  • Bump version 3.0.3 -> 3.0.4 by @mberacochea in https://github.com/EBI-Metagenomics/miassembler/pull/55

Full Changelog: https://github.com/EBI-Metagenomics/miassembler/compare/v3.0.3...v3.0.4

- Nextflow
Published by mberacochea 5 months ago

miassembler - v3.0.3 - Bugfix release - bwa-mem2 memory issues

What's Changed

  • Bugfix/decontamination seq grep by @mberacochea in https://github.com/EBI-Metagenomics/miassembler/pull/50
  • Ddds additional retry (with more ram) for bwa-mem2 host decontamination by @jmattock5 in https://github.com/EBI-Metagenomics/miassembler/pull/52

Full Changelog: https://github.com/EBI-Metagenomics/miassembler/compare/v3.0.2...v3.0.3

- Nextflow
Published by mberacochea 5 months ago

miassembler - v3.0.2

What's Changed

  • Bugfix/decontamination seq grep by @mberacochea in https://github.com/EBI-Metagenomics/miassembler/pull/50

Full Changelog: https://github.com/EBI-Metagenomics/miassembler/compare/v3.0.1...v3.0.2

- Nextflow
Published by SandyRogers 6 months ago

miassembler - v3.0.1

What's Changed

  • Set different quality thresholds for ONT and PacBio by @Ge94 in https://github.com/EBI-Metagenomics/miassembler/pull/43
  • Add additional retry (with more ram) for bwa-mem2 index by @SandyRogers in https://github.com/EBI-Metagenomics/miassembler/pull/45

Full Changelog: https://github.com/EBI-Metagenomics/miassembler/compare/v.3.0.0...v3.0.1

- Nextflow
Published by Ge94 6 months ago

miassembler - v3.0.0

Massive work from @ochkalova and @jmattock5

What's Changed

  • Add --iontorrent by @KateSakharova in https://github.com/EBI-Metagenomics/miassembler/pull/40
  • Increase memory for CANU LR by @KateSakharova in https://github.com/EBI-Metagenomics/miassembler/pull/41
  • Add more time to CANU LR by @KateSakharova in https://github.com/EBI-Metagenomics/miassembler/pull/42
  • Fix existing tests by @Ge94 in https://github.com/EBI-Metagenomics/miassembler/pull/46
  • Added a skiphumandecontamination flag - not to be used much. by @mberacochea in https://github.com/EBI-Metagenomics/miassembler/pull/47
  • Feature/contig decontamination by @ochkalova in https://github.com/EBI-Metagenomics/miassembler/pull/44
  • update version number to 3.0.0 by @ochkalova in https://github.com/EBI-Metagenomics/miassembler/pull/48

New Contributors

  • @ochkalova made their first contribution in https://github.com/EBI-Metagenomics/miassembler/pull/44

Full Changelog: https://github.com/EBI-Metagenomics/miassembler/compare/v2.0.0...v3.0.0

- Nextflow
Published by mberacochea 7 months ago

miassembler - v2.0.0

What's Changed

  • Added decontamination by reference genome on top of host by @mberacochea in https://github.com/EBI-Metagenomics/miassembler/pull/10
  • MultiQC reports per run set and per study by @mberacochea in https://github.com/EBI-Metagenomics/miassembler/pull/13
  • Support external data through samplesheet by @KateSakharova in https://github.com/EBI-Metagenomics/miassembler/pull/11
  • Fire specific config to access external data by @mberacochea in https://github.com/EBI-Metagenomics/miassembler/pull/14
  • Improved QC and inclusion of end of execution reports by @mberacochea in https://github.com/EBI-Metagenomics/miassembler/pull/15
  • Improvement of the retry-with-more-memory logic by @SandyRogers in https://github.com/EBI-Metagenomics/miassembler/pull/19
  • Structure refactor to support both long reads and short reads by @mberacochea in https://github.com/EBI-Metagenomics/miassembler/pull/17
  • Addition of long-reads pre-assembly qcs by @Ge94 in https://github.com/EBI-Metagenomics/miassembler/pull/16
  • Fix for the filter ratio threshold logic by @jmattock5 in https://github.com/EBI-Metagenomics/miassembler/pull/22
  • Private fire support by @mberacochea in https://github.com/EBI-Metagenomics/miassembler/pull/23
  • Update published contigs by @Ge94 in https://github.com/EBI-Metagenomics/miassembler/pull/25
  • Include the calculation of a single coverage and coverage depth value by @mberacochea in https://github.com/EBI-Metagenomics/miassembler/pull/28
  • Added exception for empty contig file by @Ge94 in https://github.com/EBI-Metagenomics/miassembler/pull/30
  • Added megahit graph to output files by @Ge94 in https://github.com/EBI-Metagenomics/miassembler/pull/29
  • General bug fixes in miassembler by @Ge94 in https://github.com/EBI-Metagenomics/miassembler/pull/31
  • Patched the bwamem2 retry policy by @mberacochea in https://github.com/EBI-Metagenomics/miassembler/pull/33
  • Bugfix in decontamination step - remove extra column from blast output by @Ge94 in https://github.com/EBI-Metagenomics/miassembler/pull/34
  • Added full support for long reads by @Ge94 in https://github.com/EBI-Metagenomics/miassembler/pull/24
  • Minor reorganization of docs and removed some debug files by @mberacochea in https://github.com/EBI-Metagenomics/miassembler/pull/38
  • Update schema_input.json with flye by @KateSakharova in https://github.com/EBI-Metagenomics/miassembler/pull/39

New Contributors

  • @SandyRogers made their first contribution in https://github.com/EBI-Metagenomics/miassembler/pull/19
  • @jmattock5 made their first contribution in https://github.com/EBI-Metagenomics/miassembler/pull/22

Full Changelog: https://github.com/EBI-Metagenomics/miassembler/compare/v1.0.0...v2.0.0

- Nextflow
Published by Ge94 10 months ago

miassembler - v1.0.0

What's Changed

  • Update of resource assignments per module by @Ge94 in https://github.com/EBI-Metagenomics/miassembler/pull/3
  • Added support for metatranscriptomics and private data by @Ge94 in https://github.com/EBI-Metagenomics/miassembler/pull/4
  • Some tweaks on top of the restructure_outputs branch. by @mberacochea in https://github.com/EBI-Metagenomics/miassembler/pull/7
  • Feature/restructure outputs by @KateSakharova in https://github.com/EBI-Metagenomics/miassembler/pull/6
  • Fix the coverage report, we were using the samtools flags for decont. instead of mapping by @mberacochea in https://github.com/EBI-Metagenomics/miassembler/pull/8
  • Refactor the single_end meta thing to be pulled from the ENA metadata. by @mberacochea in https://github.com/EBI-Metagenomics/miassembler/pull/9

New Contributors

  • @KateSakharova made their first contribution in https://github.com/EBI-Metagenomics/miassembler/pull/6

Full Changelog: https://github.com/EBI-Metagenomics/miassembler/compare/v1.0.0-beta...v1.0.0

- Nextflow
Published by mberacochea over 1 year ago

miassembler - First pre-release

This is the first pre-release of the EBI Metagenomics assembly pipeline in nextflow, miassembler. It currently supports short read assembly preceded by read qc with fastp, and pre- and post-assembly host decontamination.

- Nextflow
Published by Ge94 over 1 year ago