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Dev -> Master for v3.6 release#773

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Merged

drpatelh merged 44 commits intomasternf-core/rnaseq:masterfrom devnf-core/rnaseq:devCopy head branch name to clipboardMar 4, 2022

+1,431-1,030

Commits

Commits on Dec 17, 2021

• Bump pipeline version to 3.6dev

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• Merge pull request #747 from drpatelh/bump

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Commits on Feb 10, 2022

• Patch RSEM_PREPAREREFERENCE configuration

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• Rename RSEM_PREPAREREFERENCE_TRANSCRIPTS to MAKE_TRANSCRIPTS_FASTA

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• Merge pull request #763 from mahesh-panchal/patch_rsem_config

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Commits on Feb 14, 2022

• Simplify process selectors in modules.config and quote everything

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  4142ec8

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• Adjust spacing

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  684b4f4

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• Run nf-core modules update

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  01de13e

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• Add when statement to local modules

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  3281aeb

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• Bump MultiQC version

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  f97169e

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• Revert MultiQC bump because something else broke

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  79b5c16

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• Revert contentious process selectors in modules.config

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Commits on Feb 15, 2022

• Merge pull request #766 from drpatelh/update

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• Template update for nf-core/tools version 2.3.dev0

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  96f6b72

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• Fix merge conflicts

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  28ef98c

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• Sync pipeline with nf-core/tools dev to fix linting

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  8fba444

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• Fix linting

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  accb04b

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• Fix linting again

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Commits on Feb 17, 2022

• Update usage docs

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  b7a34cb

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• Update footnotes in usage docs

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  d04519c

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• Add NFCORE_RNASEQ prefix everywhere

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  b66f055

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• Merge pull request #767 from drpatelh/template

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Commits on Feb 20, 2022

• Add --publish_dir_mode back into pipeline #752

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  df102cd

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• Fix #759

  drpatelh

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  71c0d38

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• Fix #744

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• Update CHANGELOG

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  24c69fb

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• Fix ECLint

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  6775dc3

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• Fix process selector for CUSTOM_GETCHROMSIZES

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  091f952

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• Fix #753

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  a7915a6

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• Fix ECLint

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  f1146a2

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• Easy fix for #754

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Commits on Feb 21, 2022

• Merge pull request #770 from drpatelh/updates

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• Fix #769

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  210069d

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• Fix #750

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  1f97e57

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• Refactor modules.config for optional rseqc modules

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• Make --outdir mandatory

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  c3313c0

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• Fix linting

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Commits on Feb 22, 2022

• Use modulo operation instead to get read number

  drpatelh

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  e09cde4

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• Tweak Groovy syntax

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  738299e

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• Remove indentation for RSEQC logic in modules.config

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  3016c0b

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• Merge pull request #771 from drpatelh/updates

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Commits on Feb 25, 2022

• Bump pipeline version to 3.6

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  9b1cc4b

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• Merge pull request #772 from drpatelh/updates

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Commits on Mar 4, 2022

• Update CHANGELOG.md

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