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PR for release 1.1.0#85

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KevinMenden merged 199 commits intomasternf-core/smrnaseq:masterfrom devnf-core/smrnaseq:devCopy head branch name to clipboardJun 15, 2021

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Commits

Commits on Jul 13, 2018

• Added basic shell of documentation

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Commits on Jun 20, 2019

• fix authors

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• fix authors

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Commits on Jun 25, 2019

• fix title

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• fix manifest

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Commits on Jun 27, 2019

• fix markdown lint

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Commits on Jul 8, 2019

• Merge pull request #18 from lpantano/TEMPLATE

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Commits on Jan 13, 2020

• Merge branch 'dev' of github.com:nf-core/smrnaseq

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Commits on Jan 16, 2020

• small doc fix

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Commits on Feb 7, 2020

• Merge pull request #34 from KevinMenden/master

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Commits on Feb 11, 2020

• make sure one file is used in collapse step

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• add changelog updates and new version

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Commits on Feb 12, 2020

• add social preview image

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• update CHANGELOG

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• remove links to non-existing 1.0 releases

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Commits on Feb 20, 2020

• Template update for nf-core/tools version 1.9

  

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Commits on Mar 1, 2020

• custom protocol implementation

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• improved --protocol documentation

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Commits on Mar 31, 2020

• update docker with new packages to migrate to new template

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• update changelog

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Commits on Apr 1, 2020

• Merge pull request #45 from nf-core/lpantano-patch-docker

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Commits on Apr 2, 2020

• Merge branch 'TEMPLATE' into dev

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• update Docker env path

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Commits on Apr 3, 2020

• get docker working

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• Merge branch 'lpantano-patch-docker' into dev

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• Update changelog

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• Merge branch 'lpantano-patch-docker' into dev

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• Merge pull request #46 from nf-core/lpantano-patch-docker

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Commits on Apr 14, 2020

• update change log

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• fix markdown linting errors

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Commits on Apr 15, 2020

• Merge pull request #47 from nf-core/lpantano-patch-update-to-latest

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Commits on Jul 30, 2020

• Template update for nf-core/tools version 1.10.1

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Commits on Jul 31, 2020

• Template update for nf-core/tools version 1.10.2

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Commits on Aug 25, 2020

• added mirdeep2

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Commits on Aug 31, 2020

• Update main.nf

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• Update edgeR_miRBase.r

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• Update main.nf

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• Update main.nf

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• Update main.nf

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Commits on Sep 21, 2020

• changed multiple files

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• updated readme.md

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Commits on Sep 28, 2020

• update base.config

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Commits on Sep 29, 2020

• fixed skip_mirdeep

  

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Commits on Sep 30, 2020

• chenged main.ng

  

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Commits on Oct 6, 2020

• changed skip_mirdeep

  

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• Update base.config

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• changed skip_mirdeep

  

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• Merge branch 'master' of https://github.com/lcabus-flomics/smrnaseq

  

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• updated skip_mirdeep

  

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Commits on Oct 8, 2020

• Update output.md

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• Update output.md

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• Update output.md

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Commits on Oct 9, 2020

• Update test.config

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Commits on Oct 16, 2020

• Update help text in main.nf

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• Update igenomes.config

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• Changed --refgenome for --fasta

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• Update main.nf

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• Update nextflow.config

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Commits on Oct 19, 2020

• Update base.config

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• Update base.config

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• Update test.config

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• Update test.config

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• Update test.config

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• Update test.config

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Commits on Oct 21, 2020

• fixed PR

  

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• Update nextflow.config

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• Update docs/output.md

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• Delete awsbatch.config

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Commits on Oct 27, 2020

• Template update for nf-core/tools version 1.11

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Commits on Nov 4, 2020

• Merge pull request #52 from lcabus-flomics/master

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• Update main.nf

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• Merge pull request #54 from lcabus-flomics/master

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Commits on Nov 6, 2020

• Merge branch 'dev' of github.com:nf-core/smrnaseq into master

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• Remove very old installation docs

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• Manually fix merge conflicts

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• Replace --reads with --input

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• Remove params.single_end

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• Bump version to 1.1dev and add skeleton schema

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• Moved parameter documentation from usage.md to pipeline schema.

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• Updated CamelCase and Upper Case parameters to be lower_case_snake_make

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Commits on Nov 7, 2020

• Tweaks to the conda environment

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• Merge branch 'dev' into custom-protocol-patch

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• Merge pull request #42 from sirselim/custom-protocol-patch

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• Merge upstream dev

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• Schema docs and changelog for --protocol custom

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Commits on Nov 10, 2020

• Merge pull request #55 from ewels/template-merge

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• Merge branch 'dev' into dev

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Commits on Nov 11, 2020

• Merge pull request #38 from MaxUlysse/dev

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• Merge branch 'dev' into lpantano-patch-i35

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• Merge pull request #36 from nf-core/lpantano-patch-i35

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Commits on Nov 12, 2020

• Add s3 data paths to test_full.config

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• Add new profile for test_full

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• Found several params missing from nextflow.config

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Commits on Nov 16, 2020

• Added params.mirtrace_species to all genomes in igenomes.config

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• Update GitHub Actions CI workflows

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• miRBase mature / hairpin - default to miRBase FTP URLs

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• Update pipeline schema help for params.mature and params.hairpin

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• Refactor init code for params.mirna_gtf

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• Changelog

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• Improve docs for params.mirna_gtf

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• Code cleanup

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Commits on Nov 19, 2020

• Template update for nf-core/tools version 1.12

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Commits on Nov 23, 2020

• Merge pull request #57 from ewels/aws-megatests

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Commits on Nov 24, 2020

• Remove duplicate parameters

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• Improve error message for missing params.fasta

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Commits on Dec 3, 2020

• Template update for nf-core/tools version 1.12.1

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Commits on Dec 10, 2020

• Merge pull request #59 from nf-core/remove-dup-params

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Commits on Dec 18, 2020

• Use -f flag with gunzip to deal with soft-links

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• Fix merge conflicts

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• Merge branch 'dev' of https://github.com/nf-core/smrnaseq into gzip

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• Update CHANGELOG

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• Rename files if unzipped

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• Merge pull request #61 from drpatelh/gzip

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Commits on Jan 27, 2021

• Use custom genome and fix nt in FASTA

  

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Commits on Feb 19, 2021

• update changelog

  

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• Merge pull request #65 from nf-core/lpantano-patch-63

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Commits on Feb 24, 2021

• Removed reference to releases before v1.0.0 and added headings for added

  

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• Fixed blank lines around headings

  

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• Removed trailing whitespace

  

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• Added inline links to release

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• Removed release reference that was replaced with inline reference.

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• Added inline links to original pipeline and current pipeline.

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• Merge pull request #66 from pericsson/update_changelog

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• Fix "seqcluster" typo

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Commits on Mar 8, 2021

• Speed up bowtie-build using multithreading

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• Forgot escape char

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• Merge branch 'master' into patch-1

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Commits on Mar 18, 2021

• Template update for nf-core/tools version 1.13

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Commits on Mar 19, 2021

• Template update for nf-core/tools version 1.13.1

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Commits on Mar 23, 2021

• Template update for nf-core/tools version 1.13.2

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Commits on Mar 25, 2021

• Template update for nf-core/tools version 1.13.3

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Commits on Apr 12, 2021

• Merge remote-tracking branch 'origin/dev' into mjsteinbaugh/master

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Commits on Apr 13, 2021

• Merged changes from nf-core template

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• Fix lint test: 'files_unchanged'

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• Fix lint test failing due to 'single_end' missing in schema

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• Fix failing lint tests 'files_unchanged'

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• Remove redundant TODOs

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Commits on Apr 14, 2021

• Remove 'single_end' and add 'custom_config_profile'

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• Empty string -> null

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• Merge pull request #69 from kstawiski/patch-1

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• Add Phil's suggestions

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Commits on Apr 26, 2021

• feat: remove social preview image to use GitHub OpenGraph

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• Merge pull request #78 from maxulysse/dev

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Commits on May 4, 2021

• remove space in genome header and special nt in hairpin for mirdeep2 to work

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• adding changes made to CHANGELOG.md

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Commits on May 6, 2021

• install libtbb2 in container

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• Update .github/workflows/ci.yml

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• Merge pull request #74 from ErikDanielsson/merging-template-updates

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• Merge branch 'master' into fix-bowtie-pr

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• Apply suggestions from code review

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• Merge pull request #75 from nf-core/fix-bowtie-pr

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• Revert to use a perl regex, but with additional characters

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• Merge upstream changes, fix conflicts

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• lint generated files

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• Merge branch 'dev' of https://github.com/sdjebali/smrnaseq into dev

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Commits on May 7, 2021

• more flexible mirtrace protocol selection

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• added trim_galore_max_length option

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• solved memory usage issues

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• updated schema

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• Merge pull request #81 from KevinMenden/dev

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• remove spaces in genome headers

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Commits on May 10, 2021

• updated mirtrace in software versions

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• Update main.nf

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• Update main.nf

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• update mirtrace process

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• Merge pull request #82 from KevinMenden/dev

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• Merge pull request #83 from KevinMenden/dev

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• Template update for nf-core/tools version 1.14

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• Merge pull request #84 from nf-core/nf-core-template-merge-1.14

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• cleaned up parameters

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• changelog

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• fixed bug; updated some versions

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• Merge pull request #86 from KevinMenden/dev

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• added custom into protocol enum

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• Merge pull request #87 from KevinMenden/dev

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• Update nextflow.config

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• fixed nfcoreschema bug

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• Merge branch 'dev' of https://github.com/KevinMenden/smrnaseq into dev

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• fixed edgeR mirbase bug (1 sample)

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• Merge branch 'dev' of https://github.com/nf-core/smrnaseq into dev

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• additional check in edgeR script

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• remove gtf from schema

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• Merge pull request #91 from KevinMenden/dev

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• update release date

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