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Dev -> Master for v3.6 release #773

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merged 44 commits into from
Mar 4, 2022
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607cf39
Bump pipeline version to 3.6dev
drpatelh Dec 17, 2021
288aa25
Merge pull request #747 from drpatelh/bump
drpatelh Dec 17, 2021
3fdd664
Patch RSEM_PREPAREREFERENCE configuration
mahesh-panchal Feb 10, 2022
7f14e06
Rename RSEM_PREPAREREFERENCE_TRANSCRIPTS to MAKE_TRANSCRIPTS_FASTA
mahesh-panchal Feb 10, 2022
e75cb15
Merge pull request #763 from mahesh-panchal/patch_rsem_config
drpatelh Feb 10, 2022
4142ec8
Simplify process selectors in modules.config and quote everything
drpatelh Feb 14, 2022
684b4f4
Adjust spacing
drpatelh Feb 14, 2022
01de13e
Run nf-core modules update
drpatelh Feb 14, 2022
3281aeb
Add when statement to local modules
drpatelh Feb 14, 2022
f97169e
Bump MultiQC version
drpatelh Feb 14, 2022
79b5c16
Revert MultiQC bump because something else broke
drpatelh Feb 14, 2022
57792a6
Revert contentious process selectors in modules.config
drpatelh Feb 14, 2022
03e774a
Merge pull request #766 from drpatelh/update
drpatelh Feb 15, 2022
96f6b72
Template update for nf-core/tools version 2.3.dev0
drpatelh Feb 15, 2022
28ef98c
Fix merge conflicts
drpatelh Feb 15, 2022
8fba444
Sync pipeline with nf-core/tools dev to fix linting
drpatelh Feb 15, 2022
accb04b
Fix linting
drpatelh Feb 15, 2022
41218aa
Fix linting again
drpatelh Feb 15, 2022
b7a34cb
Update usage docs
drpatelh Feb 17, 2022
d04519c
Update footnotes in usage docs
drpatelh Feb 17, 2022
b66f055
Add NFCORE_RNASEQ prefix everywhere
drpatelh Feb 17, 2022
4f3ec49
Merge pull request #767 from drpatelh/template
drpatelh Feb 17, 2022
df102cd
Add --publish_dir_mode back into pipeline #752
drpatelh Feb 20, 2022
71c0d38
Fix #759
drpatelh Feb 20, 2022
d55892b
Fix #744
drpatelh Feb 20, 2022
24c69fb
Update CHANGELOG
drpatelh Feb 20, 2022
6775dc3
Fix ECLint
drpatelh Feb 20, 2022
091f952
Fix process selector for CUSTOM_GETCHROMSIZES
drpatelh Feb 20, 2022
a7915a6
Fix #753
drpatelh Feb 20, 2022
f1146a2
Fix ECLint
drpatelh Feb 20, 2022
47814c9
Easy fix for #754
drpatelh Feb 20, 2022
ed4fd3e
Merge pull request #770 from drpatelh/updates
drpatelh Feb 21, 2022
210069d
Fix #769
drpatelh Feb 21, 2022
1f97e57
Fix #750
drpatelh Feb 21, 2022
fb44c5e
Refactor modules.config for optional rseqc modules
drpatelh Feb 21, 2022
c3313c0
Make --outdir mandatory
drpatelh Feb 21, 2022
03d1789
Fix linting
drpatelh Feb 21, 2022
e09cde4
Use modulo operation instead to get read number
drpatelh Feb 22, 2022
738299e
Tweak Groovy syntax
drpatelh Feb 22, 2022
3016c0b
Remove indentation for RSEQC logic in modules.config
drpatelh Feb 22, 2022
386bda0
Merge pull request #771 from drpatelh/updates
drpatelh Feb 22, 2022
9b1cc4b
Bump pipeline version to 3.6
drpatelh Feb 25, 2022
7c7f03e
Merge pull request #772 from drpatelh/updates
drpatelh Feb 25, 2022
f37d505
Update CHANGELOG.md
drpatelh Mar 4, 2022
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Update CHANGELOG.md
drpatelh authored Mar 4, 2022

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commit f37d505b995df53986a143a47c6418b6a838281e
2 changes: 1 addition & 1 deletion CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -3,7 +3,7 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [[3.6](https://github.com/nf-core/rnaseq/releases/tag/3.6)] - 2022-03-01
## [[3.6](https://github.com/nf-core/rnaseq/releases/tag/3.6)] - 2022-03-04

### Enhancements & fixes