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Updrate main with dev#27

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mberacochea wants to merge 43 commits intomainEBI-Metagenomics/miassembler:mainfrom devEBI-Metagenomics/miassembler:devCopy head branch name to clipboard

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Commits on Sep 2, 2024

• Addition of long-reads pre-assembly qcs

  Ge94

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Commits on Sep 3, 2024

• Adapt params to short/long reads workflows

  Ge94

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• Debug missed parameters

  Ge94

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• Remove extra parameters from tests

  Ge94

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• Remove extra parameter from test

  Ge94

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• Add ref genome folder to schema

  Ge94

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• WIP - Restructure the pipeline to support Long Reads and Short Reads

  mberacochea

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• Remove debug println statements

  mberacochea

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Commits on Sep 6, 2024

• add dbs links

  KateSakharova

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Commits on Sep 8, 2024

• Add db generation instructions to README

  Ge94

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Commits on Sep 16, 2024

• Merge pull request #18 from EBI-Metagenomics/fix-readme

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  KateSakharova

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Commits on Sep 17, 2024

• Bugfix/assembler memory (#19)

  SandyRogers

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  d63ce26

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Commits on Oct 25, 2024

• LR-SR miassembler merge working

  Ge94

  committed
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Commits on Oct 28, 2024

• Resolved conflicts

  Ge94

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  d129cef

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• Updated conflict params and flags after merging

  Ge94

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Commits on Nov 1, 2024

• Fixed tests, refined variables, harmonised SR+LR

  Ge94

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Commits on Nov 6, 2024

• Updated reference_genome param

  Ge94

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• Remove puthi.conf file that was pushed by accident.

  mberacochea

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• Merge pull request #17 from EBI-Metagenomics/feature/long_reads_support_structure_refactor

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  mberacochea

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Commits on Nov 7, 2024

• Update raw_reads qc script with json parser

  Ge94

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• Comment and update --platform

  Ge94

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• Minor refinements and documentation

  Ge94

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  c2a2bb6

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• Resolve conflicts

  Ge94

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Commits on Nov 13, 2024

• Fixed tests and configs

  Ge94

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Commits on Nov 14, 2024

• Merge pull request #16 from EBI-Metagenomics/feature/long_read_qc

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  mberacochea

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Commits on Nov 20, 2024

• amended filter ratio threshold to 10%

  

  Jennifer Mattock

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• Update nextflow_schema.json

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  jmattock5

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• Merge pull request #22 from EBI-Metagenomics/filter_operator

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  jmattock5

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• WIP - EBI FIRE S3 module for embargoed data

  mberacochea

  committed
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• Fire - private study - test case works on my laptop :)

  mberacochea

  committed
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Commits on Nov 21, 2024

• Add docs around private studies and one shallow test

  mberacochea

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• Merge dev

  mberacochea

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• Adjust the version on the wf metadata

  mberacochea

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• Massive commit, sorry about that.

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  mberacochea

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• Adjust code based on feedback

  mberacochea

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• Adjust code based on feedback

  mberacochea

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• Add nf-core version to .nf-core.yml

  mberacochea

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• Bump version of nf-test for nf_tests github aciton

  mberacochea

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• Adjust test - megahit with empty contigs will succedd

  mberacochea

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• Merge pull request #23 from EBI-Metagenomics/feature/private-fire-support

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  mberacochea

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Commits on Dec 10, 2024

• Merge branch 'dev' into feature/single-coverage-and-coverage-depth

  mberacochea

  committed
  f29e229

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• Retrofit some fixes

  mberacochea

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Commits on Dec 11, 2024

• Merge pull request #28 from EBI-Metagenomics/feature/single-coverage-and-coverage-depth

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  mberacochea

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