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Release 0.7#116

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muffato wants to merge 67 commits intomainsanger-tol/blobtoolkit:mainfrom devsanger-tol/blobtoolkit:devCopy head branch name to clipboard

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Commits

Commits on Sep 13, 2024

• Update sanger_test_full.yml

  Show description for 2584645
  gq1

  authored
  2584645

Commits on Sep 16, 2024

• Update sanger_test_full.yml

  Show description for ea1b05a
  gq1

  authored
  ea1b05a

• Merge pull request #113 from sanger-tol/small_tower_compute_env

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  gq1

  authored
  e0bf8ba

Commits on Sep 19, 2024

• Fixed the comment

  muffato

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  d13d1ed

• UPDATEBLOBDIR needs to pass the tsv files through certain arguments

  muffato

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  2c793aa

• Populate as much as possible of the metadata at the beginning

  muffato

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• Also generate TSV files

  muffato

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• Example plugging the TSV files into blobtools commands

  muffato

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• Skip BLOBTOOLKIT_METADATA as we generate the yaml file correctly from the beginning

  muffato

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Commits on Sep 20, 2024

• Introduced a new samplesheet parameter to track single/paired readsets

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• Populate as much as possible of the metadata at the beginning

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• Version bumps

  muffato

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• Updated the documentation

  muffato

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• Version bump

  muffato

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• Publish the windowmasker outputs too

  muffato

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  51985ad

Commits on Sep 23, 2024

• Convert input BAM/CRAM files to Fasta on the fly

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  muffato

  committed
  f47dd16

Commits on Sep 26, 2024

• Bumped the version down

  muffato

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• Pin the version of editorconfig like in the readmapping pipeline

  muffato

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• Exclude sqlite databases from ECLint

  muffato

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Commits on Sep 30, 2024

• add exclusions for nf-core lint

  tkchafin

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• Update CITATIONS.md

  tkchafin

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• prettier linting

  tkchafin

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Commits on Oct 2, 2024

• The release is going to happen today

  muffato

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• Decreased the runtime requirements for illumina alignments

  muffato

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• Wording of the changelog

  muffato

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• Merge pull request #114 from sanger-tol/chrom_view

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  muffato

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• Documentation update

  muffato

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Commits on Oct 14, 2024

• Bumped up the underlying BTK version because 4.3.9 had a bug

  muffato

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• Updated the blastn runtime requirements to avoid basement jobs

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  muffato

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  dfb4655

• database parameterisation and separate tests from sanger infrastructure

  tkchafin

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Commits on Oct 16, 2024

• Merge pull request #117 from sanger-tol/misc_fixes

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  tkchafin

  authored
  93bda84

Commits on Oct 19, 2024

• Updated database installation instructions

  muffato

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  ea6d70a

• fix URL not found in uniprot ref ftp path

  tkchafin

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• fix ftp path for taxdump

  tkchafin

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Commits on Oct 21, 2024

• Merge pull request #118 from sanger-tol/db_install

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  tkchafin

  authored
  b9bcef6

Commits on Oct 24, 2024

• Update test.config

  tkchafin

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Commits on Nov 4, 2024

• Merge pull request #120 from sanger-tol/blastn_test

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  tkchafin

  authored
  8d2b83f

Commits on Nov 11, 2024

• separate databases from sanger infra; handle compression

  tkchafin

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• Merge pull request #3 from tkchafin/dev

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  tkchafin

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  2afc63d

Commits on Nov 19, 2024

• Update conf/test_full.config

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  tkchafin

  and

  muffato

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  6399d0a

• Update subworkflows/local/input_check.nf

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  tkchafin

  and

  muffato

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• remove local database copies from assets

  tkchafin

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• remove pre-download from ci

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• docs update

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• changelog update

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• prettier linting

  tkchafin

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• remove local files from CI

  tkchafin

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• modules partially updated; stuck on samtools/view

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Commits on Nov 21, 2024

• all modules updated exc. BUSCO

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• busco updated and patched

  tkchafin

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• cleanup ignored file

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Commits on Nov 22, 2024

• Update docs/usage.md

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  tkchafin

  and

  muffato

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  7cfbcc0

• Merge pull request #121 from tkchafin/db_params

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  tkchafin

  authored
  301bcff

• bugfix: this transformation should only apply on directories (that come from UNTAR)

  muffato

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  127ea41

• Merge pull request #125 from sanger-tol/db_params

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  muffato

  authored
  01007ab

• bugfix: the blastp and blastx paths can have the same name

  muffato

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• prettier linting

  tkchafin

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• Removed references to "defaults"

  muffato

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• Merge pull request #127 from sanger-tol/db_params

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  muffato

  authored
  6fe1861

Commits on Nov 25, 2024

• Updated the modules

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• Merge branch 'dev' into anaconda_purge_2

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• Updated a few more references to Anaconda

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• Updated the changelog too

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• [prettier]

  muffato

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• Merge pull request #124 from tkchafin/anaconda_purge_2

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  tkchafin

  authored
  000b442

Commits on Dec 16, 2024

• Update ci.yml

  tkchafin

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• Merge pull request #130 from sanger-tol/ci

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  tkchafin

  authored
  81d26b4