Code

Release 2.0#16

Code

Merged

muffato merged 96 commits intomainsanger-tol/insdcdownload:mainfrom devsanger-tol/insdcdownload:devCopy head branch name to clipboardJun 4, 2024

+1,155-546

Commits

Commits on Oct 7, 2022

• .first() is not needed

  muffato

  committed
  6615371

Commits on Oct 8, 2022

• Version bump

  muffato

  committed
  cf0e48f

Commits on Dec 3, 2022

• add missing light logo image in assets directory

  gq1

  committed
  b63474e

• resize logo image size in html email

  gq1

  committed
  cd0c710

Commits on Dec 4, 2022

• reduce the logo image furthrer and show the full size in the email html template

  gq1

  committed
  ba63ceb

Commits on Dec 5, 2022

• Merge pull request #3 from sanger-tol/fix-email-html-template

  Show description for 0695970
  muffato

  authored
  0695970

Commits on Dec 7, 2022

• Create tower_lsf_full_tests.yml

  gq1

  authored
  6c418ed

Commits on Dec 8, 2022

• Update tower_lsf_full_tests.yml

  Show description for 33e89e3
  gq1

  authored
  33e89e3

• Update and rename tower_lsf_full_tests.yml to sangerfulltest.yml

  Show description for 6a8820f
  gq1

  authored
  6a8820f

• Create sangertest.yml

  Show description for afd58b6
  gq1

  authored
  afd58b6

Commits on Dec 12, 2022

• Update sangerfulltest.yml

  Show description for f0f1c95
  gq1

  authored
  f0f1c95

• Update sangerfulltest.yml

  Show description for 10416fc
  gq1

  authored
  10416fc

Commits on Dec 13, 2022

• Update sangerfulltest.yml

  Show description for 2bacd5e
  gq1

  authored
  2bacd5e

• Update sangertest.yml

  Show description for be81880
  gq1

  authored
  be81880

Commits on Dec 14, 2022

• Update sangertest.yml

  Show description for af7588a
  gq1

  authored
  af7588a

• Update sangerfulltest.yml

  Show description for 91dcc6a
  gq1

  authored
  91dcc6a

• Merge pull request #4 from sanger-tol/LSF_Full_test

  Show description for e02c7ae
  muffato

  authored
  e02c7ae

Commits on Jan 19, 2023

• Updated logo

  muffato

  committed
  858714b

• Support compressed files too

  muffato

  committed
  d2e1045

• Imported the latest shared subworkflows

  muffato

  committed
  8ac8ff2

Commits on Jan 20, 2023

• Reordering of parameters to match the other pipelines and connect relative paths from the samplesheet to the --outdir parameter

  muffato

  committed
  0f538f9

• Exclude the gene annotation files from md5checksums.txt

  muffato

  committed
  b0212c4

• Provide a default value for --outdir

  muffato

  committed
  1c292c4

• [prettier]

  muffato

  committed
  51437fd

• nf-core lint fixes

  muffato

  committed
  9d4c07d

• Pin nf-core to 2.5 since that is the version of the template I used

  muffato

  committed
  5d2f67e

• --outdir is now mandatory

  muffato

  committed
  cf19126

• Updated the change-log

  muffato

  committed
  9bb76be

• Doc update

  muffato

  committed
  d2b5de9

Commits on Jan 23, 2023

• bugfix: was discarding species_dir

  muffato

  committed
  631688c

Commits on Feb 1, 2023

• Optimised resource usage for tabix too

  muffato

  committed
  8ab4b3a

• More information about the output files

  muffato

  committed
  fedd540

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

  muffato

  committed
  1e82b2b

• Documentation update

  muffato

  committed
  fc4a789

• Documentation update

  muffato

  committed
  3480e0a

Commits on Feb 2, 2023

• Merge branch 'full_test' into dev

  muffato

  committed
  ef540fc

Commits on Apr 13, 2023

• New cleanup profile to tidy up the integration runs on the farm

  muffato

  committed
  cf7443f

Commits on Jul 14, 2023

• Template update for nf-core/tools version 2.6

  muffato

  committed
  0a9c648

• Template update for nf-core/tools version 2.7

  muffato

  committed
  9e07b9b

• Template update for nf-core/tools version 2.8

  muffato

  committed
  93863d6

• [linting] prettier

  muffato

  committed
  bfce31f

• [linting] black

  muffato

  committed
  31e5f8c

• Merge branch 'TEMPLATE' into dev

  muffato

  committed
  ed0b297

• Merge branch 'TEMPLATE' into dev

  muffato

  committed
  9284bfb

• Merge branch 'TEMPLATE' into dev

  muffato

  committed
  bcb2b50

• Fixed the modules installation

  muffato

  committed
  23f24b7

• Fixed the modules path

  muffato

  committed
  9268ef6

Commits on Jul 15, 2023

• Now need nf-core 2.8

  muffato

  committed
  2d86b29

• we use prettier for the cff files

  muffato

  committed
  f9dadd0

• Need to use Nextflow.error

  muffato

  committed
  cb4d091

• [linting] prettier

  muffato

  committed
  4540aa1

• Fixed the Conda directives

  muffato

  committed
  931c243

• The quay.io prefix should now be skipped

  muffato

  committed
  435fcf1

• No output for Tower

  muffato

  committed
  a9551d5

• We don't use MultiQC

  muffato

  committed
  1d2524a

• Fixed the wget conda package

  muffato

  committed
  7254f04

• [linting] prettier

  muffato

  committed
  890dbb6

• was 2 before the template update

  muffato

  committed
  e903d25

• We do this through a profile

  muffato

  committed
  81178e5

• Fixed the example params.yaml

  muffato

  committed
  b540ef3

• [linting] prettier

  muffato

  committed
  9682670

• We don't make shared sanger-tol workflows anymore

  muffato

  committed
  d7951cf

• Not needed

  muffato

  committed
  f17c776

• This file is now identical

  muffato

  committed
  d3ade99

Commits on Jul 31, 2023

• Leftover from a copy

  Show description for 8d9bc1c
  

  muffato

  and

  priyanka-surana

  authored
  8d9bc1c

• Added a redirection notice to the pipeline website

  muffato

  committed
  7b33db6

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

  muffato

  committed
  c2a374f

• Added the code of conduct back

  muffato

  committed
  7777314

• There is no parameters.md page anymore

  muffato

  committed
  00badc4

• Fixed README - now matching the template and linking to the pipeline website

  muffato

  committed
  3c42dfa

Commits on Aug 4, 2023

• Updated the DOI

  muffato

  committed
  44fbe8b

• This is superfluous

  muffato

  committed
  24eea75

• Updated the contributions

  muffato

  committed
  a94039d

• Added options to submit the pipelines to the farm from GitHub

  muffato

  committed
  322ca6c

• docfix

  muffato

  committed
  e1b927d

Commits on Aug 10, 2023

• Latest nomenclature

  muffato

  committed
  e24a6f7

Commits on Aug 11, 2023

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

  Show description for aa2a366
  muffato

  authored
  aa2a366

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

  muffato

  committed
  1b7f285

Commits on Aug 14, 2023

• Use the latest version of the Tower action

  muffato

  committed
  9f16631

Commits on Aug 16, 2023

• Update sanger_test_full.yml, remove variable pipeline and upload artifacts

  gq1

  authored
  b4eb799

• Update sanger_test.yml - remove pipeline variable and upload artifacts

  gq1

  authored
  4fee623

• Update sanger_test.yml

  gq1

  authored
  706a599

• Update sanger_test_full.yml

  gq1

  authored
  231a097

• Update sanger_test.yml

  gq1

  authored
  b2c6f82

• Merge pull request #13 from sanger-tol/tower_action

  Show description for 24319dc
  gq1

  authored
  24319dc

Commits on Aug 18, 2023

• New tolsoft details

  muffato

  committed
  9c20644

• Fixed the repository name

  muffato

  committed
  c2dba62

• Merge pull request #14 from sanger-tol/new_tolsoft_details

  Show description for 93a07cf
  gq1

  authored
  93a07cf

Commits on Sep 23, 2023

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

  muffato

  committed
  403f469

Commits on Oct 4, 2023

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

  Show description for 5649f47
  muffato

  authored
  5649f47

Commits on May 24, 2024

• Version bump

  muffato

  committed
  ffe15b9

• [prettier]

  muffato

  committed
  21c81bf

Commits on Jun 3, 2024

• The default branch in main now, PR to main will fail, not master

  gq1

  authored
  6b71ac3

• Add one more unchanged file for nf-core linting

  gq1

  authored
  8ee7114

• Merge pull request #18 from sanger-tol/ci_branch

  Show description for e79c6b7
  muffato

  authored
  e79c6b7

Commits on Jun 4, 2024

• Updated the release date

  muffato

  committed
  8976796