Code

Release 2.2.0#176

Code

Merged

GallVp merged 83 commits intomainPlant-Food-Research-Open/assemblyqc:mainfrom devPlant-Food-Research-Open/assemblyqc:devCopy head branch name to clipboardNov 5, 2024

+7,712-3,033

Commits

Commits on Sep 30, 2024

• Version bumped to 2.2.0+dev

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  fdaa2f9

• Merge pull request #143 from Plant-Food-Research-Open/bump/version

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  2c5bbc4

Commits on Oct 1, 2024

• Reduced the GenomeTools stats figures to 300 DPI and set synteny_mummer_min_bundle_size to 1000000

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  bbb0177

• Updated params

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  bf337ba

• Merge pull request #144 from Plant-Food-Research-Open/optimise/report

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  GallVp

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  89b9e5a

• Added gfastats

  GallVp

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  98ff46c

• Updated changelog

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  fc0f989

• Added description for gfastats_skip

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  fba2ea0

• Merge pull request #145 from Plant-Food-Research-Open/add/gfastats

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  dd7bd92

Commits on Oct 9, 2024

• Template update for nf-core/tools version 3.0.0

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  87f4f4a

• Merge branch 'TEMPLATE' into update/template

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  929b11f

• Updated nf-core/template to 3.0.0

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  9fc7989

• Fixed schema issues

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  c81f941

• Removed unnecessary params

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  2dfe368

• Removed max resource params

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  8817696

• Fixed linting issues

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  30b8e2e

• Migrated to [email protected]

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  1404b29

• Fixed test_full issues

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  7afc159

• Removed validate_params

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  67db39d

• Updated params

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  9096eb8

• Updated CI

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  eeae0f2

• Fixed CI and linting issues

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  3946d57

• Linting fix

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  717fbf2

• Fixed nf-test

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  559266e

• Merge pull request #150 from Plant-Food-Research-Open/update/template

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  GallVp

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  97df745

• Fixed a bug where Gene score distribution graph did not appear correctly

  GallVp

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  eeaaf3f

• Fixed ci and params

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  6a77321

• Merge pull request #148 from Plant-Food-Research-Open/fix/gtplot

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  GallVp

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  6eef70b

• Template update for nf-core/tools version 3.0.1

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  966c6b2

• Updated nf-core/template to 3.0.1

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  8fd1b9e

• Updated version checks

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  d2f537c

• Deleted template version comment action

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  530734b

• Removed fix-linting action

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  b36e868

• Updated clean-up issue

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  d7f6715

Commits on Oct 10, 2024

• Merge pull request #151 from Plant-Food-Research-Open/update/template301

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  GallVp

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  68444ef

• Updated samtools faidx to 1.21

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  5e4bdf5

• Merge pull request #152 from Plant-Food-Research-Open/update/modules

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  GallVp

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  66f76ce

• Now using nf-test for pipeline level testing

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  97928c3

• Added missing modules

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  64d0cab

• Updated config selectors

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  b193a4c

• Updated snapshots to account for 4 CPUs

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  beb0c7b

• Updated tests

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  a03629a

• Merge pull request #154 from Plant-Food-Research-Open/tests/pipeline

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  4e2e23b

• Added text/html as content mime type for the report file

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  49f9a8a

• Merge pull request #155 from Plant-Food-Research-Open/mime/report

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  1030136

Commits on Oct 13, 2024

• Version string

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  f98f3c6

• Merge TEMPLATE version 3.0.2

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  fec9135

• Updated snapshots

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  05b9eed

• Merge pull request #156 from Plant-Food-Research-Open/update/template

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  GallVp

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  789ae12

Commits on Oct 14, 2024

• Added a sequence labels table below the HiC contact map

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  af9a257

• Merge pull request #157 from Plant-Food-Research-Open/hic/seqlabels

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  807ff31

• Increased memory requirement for DNADIFF to avoid SLURM OOM kills with exit code 2

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  cbbee9d

Commits on Oct 15, 2024

• Merge pull request #158 from Plant-Food-Research-Open/fix/dnadiff

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  GallVp

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  fe7b8fc

Commits on Oct 25, 2024

• Added explicit revision param to docs

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  27a8d3b

• Updated changelog

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  62e19f5

• Merge pull request #164 from Plant-Food-Research-Open/docs/rev

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  GallVp

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  abd4695

• Added parameter hic_samtools_ext_args

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  c1f83cc

• Merge pull request #165 from Plant-Food-Research-Open/hic/filter

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  GallVp

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  26025a4

Commits on Oct 31, 2024

• Added the HiC QC report to the final report

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  5c769fa

• Updated outputs

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  5f373d6

• Merge pull request #171 from Plant-Food-Research-Open/report/hicqc

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  14ca56e

• Added the fastp log to the final report

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  d4624de

• Merge pull request #172 from Plant-Food-Research-Open/report/fastp

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  GallVp

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  d410971

Commits on Nov 2, 2024

• Added orthofinder

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  2e8844d

Commits on Nov 3, 2024

• Update flowchart

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  3c2c872

• Update flowchart

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  936bb2f

Commits on Nov 4, 2024

• Updated docs

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  fb206c4

• Fixed a couple of typos

  GallVp

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  4f8222e

• Merge pull request #174 from Plant-Food-Research-Open/add/orthofinder

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  GallVp

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  10a4bd7

• Moved around test_full options

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  abd8f51

• Updated pfr params

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  c7998d6

• Updated pfr_assembly launch script

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  8fcc5ce

• Version bump and a couple of minor fixes

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  cf11c1b

• Updated PFR's Kraken 2 database to k2_pluspfp_20240904

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  af5c449

• Increased memory requirement for Kraken 2 to 256.GB

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  e140509

• Updated docs and removed resource limits from test_full

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  d98384a

• Updated synteny_mummer_min_bundle_size for pfr/params

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  0da7cea

Commits on Nov 5, 2024

• Now using _JAVA_OPTIONS in module RUNASSEMBLYVISUALIZER to avoid user preferences related errors

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  e6b968f

• Now added user.home property to JAVA_OPTIONS

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  0f9a4ee

• Fixed version mismatches

  GallVp

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  ddc9aae

• Merge pull request #175 from Plant-Food-Research-Open/release/test

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  GallVp

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  8a7d09c

• Excluded included_configs from linting

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  ab0f094

• Merge pull request #177 from Plant-Food-Research-Open/fix/linting

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  GallVp

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  b4ced2a