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Add profile for ARM compatibility#1425

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pinin4fjords merged 49 commits intodevnf-core/rnaseq:devfrom arm_3.16.1nf-core/rnaseq:arm_3.16.1Copy head branch name to clipboardOct 23, 2024

+473-148

Commits

Commits on Oct 17, 2024

• appy changes for ARM

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  pabloaledo

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• Merge branch 'arm_3.16.1' into dev

  pinin4fjords

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  991637c

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• Fix up config

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  4bdae48

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• Reset environment ymls

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• Reset main.nfs with software changes only

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• Link sw configs to arm profile

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• Add process block

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• note pins

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• Remove conda overrides that were having no impact

  pinin4fjords

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Commits on Oct 18, 2024

• Use different RSEQC pin

  pinin4fjords

  committed
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• update BEDGRAPHTOBIGWIG pin

  pinin4fjords

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  4a8ed2b

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• Fix annotation

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  b86a6f9

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• Don't think we need the RSEQC pin

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  1b96eb8

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• correct ucsc

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  4e5d7a3

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• Merge pull request #1 from pinin4fjords/sw_to_conf

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  pabloaledo

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• Triage arm deps

  pinin4fjords

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• Non-igenomes STAR can use the latest star

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• remove rogue comment

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Commits on Oct 21, 2024

• update arm conf

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Commits on Oct 22, 2024

• Cut out module redundant software overrides

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• Merge pull request #2 from pinin4fjords/triage_arm

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  pabloaledo

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• Merge pull request #1414 from pabloaledo/dev

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  pinin4fjords

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• Merge branch 'dev' into arm_3.16.1

  pinin4fjords

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• Add frozen ARM builds

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• Container directives for conda overrides

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• Temporary Trimgalore override, singularity fixes for rsem processes

  pinin4fjords

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• update docs

  pinin4fjords

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  161cf95

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• Fix argument conflict between STAR versions

  pinin4fjords

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  caad7fa

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• Fix config error

  pinin4fjords

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  cdfb98b

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• Correction to star rsem

  pinin4fjords

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  524e19e

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• Merge branch 'arm_3.16.1' of github.com:nf-core/rnaseq into arm_3.16.1

  pinin4fjords

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• Refine config setup

  pinin4fjords

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  4f8de94

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• Bump trimgalore module

  pinin4fjords

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  a1d558e

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• Fix up ARM profile for updated trim-galore

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Commits on Oct 23, 2024

• Apply suggestions from code review

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• Apply suggestions from code review

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  drpatelh

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• Add notes for kraken2/ braken

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• Update docs

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  642d2a8

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• prettier

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  d9e534d

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• lint fix

  pinin4fjords

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  d4fcb56

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• [skip ci] Reorg ARM bits

  pinin4fjords

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  896dd74

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• Update arm.config

  drpatelh

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  314ea85

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• Fix syntax error

  pinin4fjords

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• Merge branch 'arm_3.16.1' of github.com:nf-core/rnaseq into arm_3.16.1

  pinin4fjords

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• revert trimgalore tweak to appease linter

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• Update pipeline-level tests

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• Merge branch 'arm_3.16.1' of https://github.com/nf-core/rnaseq into arm_3.16.1

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• Update CHANGELOG

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• Merge branch 'arm_3.16.1' of github.com:nf-core/rnaseq into arm_3.16.1

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