Code

Release 2.0#11

Code

Merged

muffato merged 85 commits intomainsanger-tol/ensemblrepeatdownload:mainfrom devsanger-tol/ensemblrepeatdownload:devCopy head branch name to clipboardJun 4, 2024

+1,226-712

Commits

Commits on Oct 19, 2022

• Version bump on dev

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  b16c113

Commits on Dec 20, 2022

• Added support for the annotation method

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  d64deb4

• Evaluate relative paths from --outdir

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  bb741a4

Commits on Jan 9, 2023

• We currently expect the extra sanger-tol lines in this file

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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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  4429a4b

Commits on Jan 13, 2023

• Removed extra }

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  9609f43

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

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  5fb68bf

Commits on Jan 14, 2023

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

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  e40fd54

Commits on Jan 16, 2023

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

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• Updated logo

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  e652647

Commits on Jan 17, 2023

• Added 130 for MEMLIMIT

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  76316f4

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

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  91e59ad

• Read properties of the fasta file, and augment meta

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  46ef3e6

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

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  3328f85

• Make prepare_repeats select the right tabix indexing thanks to the new meta keys

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  eec9154

• For comprehensiveness, provide channels for the unavailable indices

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• My convention is to have two blank lines there

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Commits on Jan 20, 2023

• Doc update

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• Updated the change-log

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  091bc85

Commits on Feb 1, 2023

• Optimised resource usage for tabix too

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  e9441a5

• 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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  28af129

• Brought some consistency

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  c9224e1

Commits on Feb 2, 2023

• Merge branch 'full_test' into dev

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  08a0350

Commits on Jul 16, 2023

• Fixed the pipeline name

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  19b9f68

• Template update for nf-core/tools version 2.6

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• Merge branch 'TEMPLATE' into dev

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  7384fb8

• Template update for nf-core/tools version 2.7

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  5321874

• 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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  a69b87f

• Fixed the pipeline description

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  efd3e8d

• Merge branch 'TEMPLATE' into dev

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  fe86440

• Fixed the pipeline description

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  8f3174b

• Merge branch 'TEMPLATE' into dev

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  9b92717

• Fixed the example params.yaml

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  fbb6993

• We do this through a profile

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  855419b

• [linting] prettier

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• [linting] black

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  dc0df2c

• modules update

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  841e44d

• Fixed the Conda directives

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  88210f7

• Fixed the wget conda package

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  89ff640

• The quay.io prefix should now be skipped

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• Not needed

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• This file is now identical

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  ca307b2

• we use prettier for the cff files

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  dc02dc1

• Now need nf-core 2.8

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  f7b0b23

• Moved from sanger-tol to local

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  e66c079

• 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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  04fbd91

Commits on Aug 4, 2023

• Updated the DOI

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  c1bb5e0

• Fixed the README

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  46d5213

• Added the code of conduct

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  e45b9b1

• Aligned with the template

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  e9f36b5

• Added some instructions about fetching the Ensembl parameters

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  4f56065

• Added the farm tests (through Tower)

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  c6d8874

• Conda syntax

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  44126ff

• Fixed the example

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  bee8e2d

• Fixed the example

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  f986da9

Commits on Aug 11, 2023

• The warning should be on the README too

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• Latest nomenclature

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  b177af0

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

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  919c1f4

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

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  d649e81

Commits on Aug 14, 2023

• Use the latest version of the Tower action

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  ec56e9b

Commits on Aug 16, 2023

• Update sanger_test.yml

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  6b9a55d

• Update sanger_test_full.yml

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  0a98259

• Update sanger_test_full.yml

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  fbdb59f

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

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  009c212

Commits on Aug 18, 2023

• New tolsoft details

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  fd35531

• Fixed the repository name

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  e6c2599

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

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  c1ef111

Commits on Sep 23, 2023

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

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  ccd9211

Commits on Oct 10, 2023

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

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  1b89a66

Commits on May 24, 2024

• Version bump

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  eb9f6bf

• Updated the output documentation

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  97516bd

• Changelog updated

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  9b0138b

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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  a6b54fa

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

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  8373ab3

Commits on Jun 4, 2024

• Updated the release date

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