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Merge dev into template sync PR #634 - #635

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Skitionek wants to merge 2040 commits into

nf-core-template-merge-4.2.1from

template-merge-634

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Merge dev into template sync PR #634#635
Skitionek wants to merge 2040 commits into
nf-core-template-merge-4.2.1from
template-merge-634

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Commits on Jul 27, 2025
- fix ro-crate
  sateeshperi
  committed
  1c22b64
- update snaps tofix multiqc llm-text nftignore
  sateeshperi
  committed
  0446e8b
Commits on Jul 28, 2025
Commits on Jul 29, 2025
- Merge pull request #556 from nf-core/new-megatests
  sateeshperi
  authored
  335f2a8
Commits on Jul 31, 2025
- bump version 4.1.0
  sateeshperi
  committed
  44e38ee
- Merge pull request #557 from sateeshperi/dev
  sateeshperi
  authored
  8cc43d8
- Merge branch 'master' into dev
  sateeshperi
  authored
  24395e2
Commits on Aug 9, 2025
Commits on Aug 10, 2025
- bump bwameth version to 0.2.9
  sateeshperi
  committed
  3be4822
- update snaps after version bumps
  sateeshperi
  committed
  5ad12a7
- update ro crate
  sateeshperi
  committed
  e09234e
- prettier fix docs
  sateeshperi
  committed
  5ded539
- fix bwameth align to allow timestamp check skip
  sateeshperi
  committed
  9889a49
- Merge pull request #561 from nf-core/feat-use-mem2-version-bumps
  sateeshperi
  authored
  73651e3
- Merge pull request #558 from nf-core/dev
  sateeshperi
  authored
  db60bfe
- bump-version 4.2.0dev
  sateeshperi
  committed
  37c5c27
Commits on Aug 11, 2025
- Merge pull request #562 from sateeshperi/dev
  sateeshperi
  authored
  c74694e
Commits on Sep 1, 2025
- Fix error in picard_bedtointervallist.config
  bounlu
  authored
  aea6b00
Commits on Sep 4, 2025
- Merge pull request #566 from nf-core/bounlu-patch-1
  sateeshperi
  authored
  4bd868d
Commits on Sep 28, 2025
- bump default and bismark tests after modules update 0.25.1
  sateeshperi
  committed
  24f742f
- update index and targeted snaps with bismark 0.25.1
  sateeshperi
  committed
  cf07b2f
Commits on Sep 30, 2025
- Merge pull request #569 from nf-core/fix-bismark-module-updates
  sateeshperi
  authored
  56f284c
Commits on Oct 15, 2025
- updated version
  eduard-watchmaker
  committed
  b8a893f
- updated version
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  a424477
- updated version
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  eb87a07
- schema
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  42f8fe0
- path
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  787282d
- path
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  320f9e2
- working version
  eduard-watchmaker
  committed
  de90b7d
Commits on Oct 21, 2025
- changed fq_align_dedup_bwamem for fq_align_bwa
  eduard-watchmaker
  committed
  8f590c7
- samtools change
  eduard-watchmaker
  committed
  cf83bb2
- taps to nfcore
  eduard-watchmaker
  committed
  7bef714
- add bam to workflow name
  eduard-watchmaker
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  c4755b5
- renaming
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  dca1e44
- changes
  eduard-watchmaker
  committed
  93abf2a
- more tests
  eduard-watchmaker
  committed
  8265979
- comment out
  eduard-watchmaker
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  9d142bf
- params
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  bb149eb
- rm file from test
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  a303797
- rm file from test
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  9ce829f
- rm file from test
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  0b69be9
Commits on Oct 22, 2025
- new parabricks fq2bam
  eduard-watchmaker
  committed
  ec22182
- fix
  eduard-watchmaker
  committed
  0051ed1
- add picard groups
  eduard-watchmaker
  committed
  8d5a482
- why only one sample
  eduard-watchmaker
  committed
  7cc8490
- why only one sample
  eduard-watchmaker
  committed
  a5fa5ae
- why only one sample
  eduard-watchmaker
  committed
  d4bbc26
- why only one sample
  eduard-watchmaker
  committed
  4e15539
- why only one sample
  eduard-watchmaker
  committed
  892598d
- why only one sample
  eduard-watchmaker
  committed
  b521204
- boradcast
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  committed
  146cb8f
Commits on Oct 23, 2025
- boradcast methyldackel
  eduard-watchmaker
  committed
  3203069
Commits on Oct 30, 2025
- updated to fastq_align_dedup_bwamem
  eduard-watchmaker
  committed
  32f5e0b
- Merge branch 'taps' of github.com:nf-core/methylseq into taps
  eduard-watchmaker
  committed
  7025f4d
- missing comma
  eduard-watchmaker
  committed
  53e636d
- rm redundant code
  eduard-watchmaker
  committed
  a06c82d
- config fix
  eduard-watchmaker
  committed
  81666bb
- forgot damn config
  eduard-watchmaker
  committed
  ffc1c2d
Commits on Nov 3, 2025
- more channels
  eduard-watchmaker
  committed
  d243263
- new snapshots
  root
  committed
  86a5349
- less tests
  eduard-watchmaker
  committed
  e254e62
- fixing new version HS metrics
  eduard-watchmaker
  committed
  48786da
- ignore multiqc parquet
  eduard-watchmaker
  committed
  ffc3ee3
- input was ahead of time lol
  eduard-watchmaker
  committed
  79fd87a
- gpu snapshhot
  root
  committed
  e959b2d
Commits on Nov 5, 2025
- fix lint issues from new template
  
  Eduard Casas
  authored and
  Eduard Casas
  committed
  4d98def
- Merge branch 'dev' into taps
  eduard-watchmaker
  authored
  7b9930c
Commits on Nov 17, 2025
- PR feedback
  
  Eduard Casas
  authored and
  Eduard Casas
  committed
  301de2e
- forgot allOf
  
  Eduard Casas
  authored and
  Eduard Casas
  committed
  a0b77aa
- paths for output
  
  Eduard Casas
  authored and
  Eduard Casas
  committed
  d7e865c
Commits on Nov 21, 2025
- update multiqc module and snapshots
  sateeshperi
  committed
  08d1bf9
- pre-commit fix all files
  sateeshperi
  committed
  8f49567
Commits on Nov 24, 2025
- Merge pull request #574 from nf-core/taps
  sateeshperi
  authored
  a41a621
Commits on Nov 26, 2025
- Merge branch 'TEMPLATE' of https://github.com/nf-core/methylseq into merging-template-updates-3.5.1
  sateeshperi
  committed
  e3dd22c
- Update multiqc module
  sateeshperi
  committed
  4a9c7cf
- Update utils_nfschema_plugin
  sateeshperi
  committed
  fff07cf
- revert downstream change
  sateeshperi
  committed
  61f2215
- lint fixes
  sateeshperi
  committed
  249ef44
- remove workflow trace succeded and snap after multiqc update
  sateeshperi
  committed
  add2c38
- revert nftignore changes and update snaps
  sateeshperi
  committed
  25008bd
- update nf-test-gpu nxf ver to 25.04.0
  sateeshperi
  committed
  ae4059f
- update nf-test gpu nxf_ver to 25.4.0
  sateeshperi
  committed
  7fefd0b
- Merge pull request #577 from sateeshperi/merging-template-updates-3.5.1
  sateeshperi
  authored
  d4fe722
Commits on Nov 27, 2025
Commits on Nov 28, 2025
Commits on Nov 29, 2025
- last changes
  eduard-watchmaker
  committed
  2629a99
Commits on Dec 1, 2025
- Merge branch 'doc-updates-taps' of github.com:nf-core/methylseq into doc-updates-taps
  sateeshperi
  committed
  02025f1
- forgot to rename conf file
  eduard-watchmaker
  committed
  8e297d5
- forgot to add conf file
  eduard-watchmaker
  committed
  1cdf17f
Commits on Dec 2, 2025
Commits on Dec 3, 2025
Commits on Dec 4, 2025
- fix: update version tracking and output for nf-core methylseq workflow
  sateeshperi
  committed
  1957d21
- chore: update changelog
  sateeshperi
  committed
  0a12198
- chore: update GPU snapshot workflow versions
  sateeshperi
  committed
  33f8db4
Commits on Dec 6, 2025
- new gpu snapshot
  EC2 Default User
  committed
  a717f8d
Commits on Dec 7, 2025
- Merge pull request #581 from nf-core/bwamem_fix
  eduard-watchmaker
  authored
  7f30dbf
- fix: add BWA_INDEX and SAMTOOLS_IDXSTATS processes, update publishDir settings
  sateeshperi
  committed
  6fdd85a
- chore: update test snapshots after skip_dedup/rrbs publishing fix
  sateeshperi
  committed
  c2caad7
- chore: update changelog for correct bam file publishing in alignments folder for --skip_deduplication and --rrbs options
  sateeshperi
  committed
  10e48fd
- new gpu snapshot
  EC2 Default User
  committed
  e56eb61
Commits on Dec 8, 2025
- Merge pull request #583 from nf-core/fix-publishing
  sateeshperi
  authored
  04f4e35
- chore: Update nf-core/methylseq to version 4.2.0
  sateeshperi
  committed
  29d224f
- Merge pull request #584 from sateeshperi/dev
  sateeshperi
  authored
  24987cc
Commits on Dec 9, 2025
- fix: Added support for the `bwamem` aligner in the AWS full test workflow configuration, ensuring compatibility with both CPU and ARM compute environments.
  sateeshperi
  committed
  f3d89d2
- Merge pull request #586 from sateeshperi/dev
  sateeshperi
  authored
  7e94991
Commits on Dec 12, 2025
- Merge pull request #585 from nf-core/dev
  sateeshperi
  authored
  5aa5646
- chore: Update nf-core/methylseq to version 4.3.0dev
  sateeshperi
  committed
  9ab5d92
- Merge pull request #590 from sateeshperi/bump-version-4.3.0
  sateeshperi
  authored
  c6babf7
Commits on Mar 24, 2026
- Update usage.md
  jdgilbert245
  authored
  4f14b72
Commits on Apr 8, 2026
- Filter Bismark coverage files in targeted sequencing mode
  FelixKrueger
  committed
  d60b41f
Commits on Apr 9, 2026
Commits on Apr 10, 2026
Commits on Jun 13, 2026
- add methurator
  edogiuili
  committed
  616fb2a
- add methurator config
  edogiuili
  committed
  35ccdd4
- add methurator to main workflow
  edogiuili
  committed
  32b72af
- add parameters for methurator
  edogiuili
  committed
  0f3ea64
- add tests for methurator
  edogiuili
  committed
  d31fb60
- update docs
  edogiuili
  committed
  32d46ea
- add t-max param
  edogiuili
  committed
  676ec76
- pass a tuple and remove version channel
  edogiuili
  committed
  8f47e90
- add methurator param to fasta_index_methylseq to create an index if methurator is specified
  edogiuili
  committed
  8c49ca7
- add ext args to the module
  edogiuili
  committed
  cae0ab7
- fix module name
  edogiuili
  committed
  cd8efc4
- change error strategy for methurator
  edogiuili
  committed
  5ec42b8
- add methurator as boolean to trigger fasta index generation
  edogiuili
  committed
  cd1f6bf
- add minimum coverage default
  edogiuili
  committed
  859cfaf
- add minimum coverage default
  edogiuili
  committed
  99462c8
- change ch_methurator_input into a tuple
  edogiuili
  committed
  010f960
- add configs into main config file
  edogiuili
  committed
  0fd5f5d
- add methurator tests and snaps
  edogiuili
  committed
  9f42afb
Commits on Jun 14, 2026
- add methurator param instead of input boolean to trigger fasta index
  edogiuili
  committed
  276b7fc
- readme update
  edogiuili
  committed
  cfa4edc
- nf-test version to 0.9.3
  edogiuili
  committed
  908ad41
- use methurator as boolean to trigger fasta index
  edogiuili
  committed
  f4682d1
- linting
  edogiuili
  committed
  471e334
Commits on Jun 15, 2026
- update methurator tests to account for unstable yml files
  edogiuili
  committed
  bbb3a80
Commits on Jul 10, 2026
- Temporary Patch for issue #607
  Deriverx2
  committed
  db75fd4
- Update Bismark to 3.0.0 and modernise alignment modules/subworkflows
  
  pinin4fjords
  and
  claude
  committed
  634119b
- Add PR number to changelog [skip ci]
  
  pinin4fjords
  and
  claude
  committed
  554b3f4
- Trigger CI
  
  pinin4fjords
  and
  claude
  committed
  fa713d6
- Remove dangling aws_batch profile to fix config parsing
  
  pinin4fjords
  and
  claude
  committed
  8ac16f3
- Pin nf-amazon plugin version
  
  pinin4fjords
  and
  claude
  committed
  6362dad
- [automated] Update GPU snapshot for tests/bwameth_use_gpu.nf.test
  nf-core-bot
  committed
  7b52baf
- Use environment.yml for FILTER_BEDGRAPH_TARGETS conda spec
  
  pinin4fjords
  and
  claude
  committed
  e77d632
- Remove stray setup-nextflow gitlink
  
  pinin4fjords
  and
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  committed
  200de44
Commits on Jul 13, 2026
- Merge branch 'dev' into aws-fix
  eduard-watchmaker
  authored
  f3e9388
- Apply suggestions from code review
  eduard-watchmaker
  authored
  f902486
- Apply suggestions from code review
  eduard-watchmaker
  authored
  4d7de75
Commits on Jul 14, 2026
- Merge pull request #610 from nf-core/update/bismark-3.0.0
  pinin4fjords
  authored
  9308ad4
Commits on Jul 15, 2026
- bismark: update modules to 3.1.0
  FelixKrueger
  committed
  d2b2449
- docs: add CHANGELOG entry for Bismark 3.1.0 bump (#614)
  FelixKrueger
  committed
  fae2851
- Merge branch 'dev' into aws-fix
  eduard-watchmaker
  authored
  5205942
- Merge pull request #613 from Deriverx2/aws-fix
  eduard-watchmaker
  authored
  f67e43c
- Merge pull request #614 from FelixKrueger/bump/bismark-3.1.0
  FelixKrueger
  authored
  ba44967
Commits on Jul 18, 2026
Commits on Jul 19, 2026
Commits on Jul 20, 2026
- fix conflicts
  edogiuili
  committed
  b49bbbc
- update changelog
  edogiuili
  committed
  e913e80
- add errorStrategy for methurator_plot
  edogiuili
  committed
  c2ec9c9
- fix error message for taps/bwamem
  edogiuili
  committed
  765ad5e
- update methurator params adding a methurator_ prefix
  edogiuili
  committed
  7c0ef64
- run test with compute_ci false by default
  edogiuili
  committed
  fee9cd2
- [automated] Update GPU snapshot for
  nf-core-bot
  committed
  dbd4726
- add methurator_ prefix
  edogiuili
  committed
  09a4a15
- fix typo
  edogiuili
  committed
  5cb14d6
- fix typo
  edogiuili
  committed
  98bbfe7
- Merge pull request #617 from FelixKrueger/feat/trimgalore-2.3.0
  FelixKrueger
  authored
  085e297
- Merge pull request #618 from FelixKrueger/fix/rastair-strict-env
  FelixKrueger
  authored
  e02171c
- Merge branch 'dev' into nf-core-template-merge-4.0.2
  FelixKrueger
  committed
  308444e
- Merge branch 'dev' into feat/combined-index-alignment
  FelixKrueger
  authored
  4104f2f
- tests: regenerate CPU snapshots for merged modules (multiqc 1.34 + Trim Galore 2.3.0)
  FelixKrueger
  committed
  780a283
- [automated] Update GPU snapshot for
  nf-core-bot
  committed
  32ca0cd
- conf: regenerate container config files for merged modules
  FelixKrueger
  committed
  206f157
- test: regenerate combined_index snapshot for Trim Galore 2.3.0
  FelixKrueger
  committed
  6839029
- Merge pull request #606 from nf-core/nf-core-template-merge-4.0.2
  FelixKrueger
  authored
  e8df423
- Merge branch 'dev' into feat/combined-index-alignment
  FelixKrueger
  authored
  9d8214f
- test: regenerate combined_index snapshot for multiqc 1.34 (post-#606 merge)
  FelixKrueger
  committed
  4081bf8
Commits on Jul 22, 2026
- update snapshots
  edogiuili
  committed
  41f6af5
- update methurator module
  edogiuili
  committed
  c83452c
- update to v2.2.0 and remove compute_ci flag
  edogiuili
  committed
  17c6da5
- Merge branch 'dev' into dev
  edogiuili
  authored
  fb9c96a
- update snaps
  edogiuili
  committed
  93d43bf
- update snaps
  edogiuili
  committed
  2fe53fd
Commits on Jul 24, 2026
- Merge pull request #616 from FelixKrueger/feat/combined-index-alignment
  FelixKrueger
  authored
  28c8fd6
- Merge branch 'dev' into dev
  FelixKrueger
  authored
  e6056bb
- register local subworflow diff
  edogiuili
  committed
  d25a9a7
- change methurator_compute_ci false by default
  edogiuili
  committed
  bd46819
- fix linting
  edogiuili
  committed
  a5a17ac
- Merge pull request #609 from edogiuili/dev
  edogiuili
  authored
  3dd7bd3
Commits on Aug 10, 2026
- Merge branch 'dev' into nf-core-template-merge-4.0.3
  FelixKrueger
  committed
  5156b3a
Commits on Aug 11, 2026
- Merge pull request #620 from nf-core/nf-core-template-merge-4.0.3
  FelixKrueger
  authored
  9855ef9
Commits on Aug 17, 2026
- Sync bismark/* modules onto upstream's intra-instance -p threading
  FelixKrueger
  committed
  721ae33
Commits on Aug 18, 2026
- tests: stop asserting the HISAT2 .1.ht2 index bytes
  FelixKrueger
  committed
  f58de56
- Merge pull request #622 from FelixKrueger/chore/bismark-modules-sync-12385
  FelixKrueger
  authored
  915959e
Commits on Sep 11, 2026
- Add manifest.diagram
  ewels
  committed
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Commits on Sep 18, 2026
- Merge pull request #624 from nf-core/metro-maps
  ewels
  authored
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Commits on Oct 28, 2026
- Merge dev into TEMPLATE
  Skitionek
  committed
  3956d1d

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