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Release 2.0#11

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muffato merged 87 commits intomainsanger-tol/ensemblgenedownload:mainfrom devsanger-tol/ensemblgenedownload:devCopy head branch name to clipboardJun 4, 2024

+1,289-603

Commits

Commits on Sep 25, 2022

• initial template build from nf-core/tools, version 2.5

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Commits on Oct 19, 2022

• Version bump on dev

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Commits on Dec 12, 2022

• Added support for the annotation method

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Commits on Dec 20, 2022

• typo

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• Documentation update

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• Added a check

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• Evaluate relative paths from --outdir

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Commits on Jan 9, 2023

• Linting: prettier, black, and updated nf-core yaml

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• Pinning the version of nf-core as long as this is a 2.5 pipeline

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• --outdir should actually be considered a mandatory parameter

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Commits on Jan 13, 2023

• Converted most "it" iterators to explicitly-named variables

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• Removed extra }

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Commits on Jan 16, 2023

• Merge pull request #2 from sanger-tol/new_ftp

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Commits on Jan 17, 2023

• Updated logo

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• Typo: assembly_name is not a recognised command-line parameter

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• Added 130 for MEMLIMIT

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• Don't complain about missing files on the Ensembl FTP

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• Read properties of the fasta file, and augment meta

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• samtools dict needs an amount of RAM proportional to the length of the longest sequence

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• Select the right tabix indexing based on the coordinates actually used in the GFF file

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• Updated tag to match the convention

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• For comprehensiveness, provide channels for the unavailable indices

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Commits on Jan 18, 2023

• Adjusted the memory requirement for sort+tabix

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Commits on Jan 20, 2023

• Updated the change-log

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• Doc update

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Commits on Feb 1, 2023

• Nextflow version bump due to the way Conda is enabled/disabled

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• Documentation update

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• Documentation update

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• Brought some consistency

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Commits on Feb 2, 2023

• Merge branch 'full_test' into dev

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Commits on Jul 15, 2023

• Template update for nf-core/tools version 2.6

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• Template update for nf-core/tools version 2.7

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• Template update for nf-core/tools version 2.8

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• Merge branch 'TEMPLATE' into dev

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• Merge branch 'TEMPLATE' into dev

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• Merge branch 'TEMPLATE' into dev

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• we use prettier for the cff files

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• Now need nf-core 2.8

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• [linting] black

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• [linting] prettier

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• module update

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• Fixed the Conda directives

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• Fixed the wget conda package

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• The quay.io prefix should now be skipped

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• Not needed

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• be consistent

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• Moved sanger-tol to local

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• No more sanger-tol shared repository

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• Fixed the example params.yaml

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• This file is now identical

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• [linting] prettier

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Commits on Jul 16, 2023

• was 2 before the template update

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• We do this through a profile

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• Not needed

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• We don't use MultiQC

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Commits on Jul 31, 2023

• The template was erroneously hardcoding sanger-tol/readmapping

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• Added a redirection notice to the pipeline website

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• The convention is now to put all the pipeline_info files in per-pipeline sub-directories

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Commits on Aug 3, 2023

• Added the code of conduct

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• Fixed the README

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• Fixed the date format

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• Added some instructions about fetching the Ensembl parameters

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• Updated the DOI

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Commits on Aug 4, 2023

• Wrong copy/paste

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• One more file now in line with the template

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• Added the farm tests (through Tower)

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• prettier

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Commits on Aug 10, 2023

• Latest nomenclature

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• The warning should be on the README too

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Commits on Aug 11, 2023

• Merge pull request #6 from sanger-tol/template_update

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• Now use "outdir", which is equivalent to a ToL analysis directory

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Commits on Aug 14, 2023

• Use the latest version of the Tower action

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Commits on Aug 16, 2023

• Update sanger_test.yml

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• Update sanger_test_full.yml

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• Update sanger_test_full.yml

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• Merge pull request #9 from sanger-tol/tower_action

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Commits on Aug 18, 2023

• New tolsoft details

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• Fixed the repository name

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• Merge pull request #10 from sanger-tol/new_tolsoft_details

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Commits on Sep 23, 2023

• Made the relation between --outdir and the samplesheet outdir clearer

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Commits on Oct 10, 2023

• Merge pull request #8 from sanger-tol/outdir

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Commits on May 24, 2024

• Version bump

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• Updated the changelog

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Commits on Jun 3, 2024

• change default branch to main for PR branch checking

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• Add one more unchanged file for nf-core linting

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• Merge pull request #12 from sanger-tol/ci_branch

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Commits on Jun 4, 2024

• Updated the release date

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