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Prepare for release 2.3.0 #208

Merged
merged 127 commits into from Apr 5, 2022
Merged

Prepare for release 2.3.0 #208

merged 127 commits into from Apr 5, 2022

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marissaDubbelaar
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This release includes an alteration of the documentation, inclusion of a new graph that explains the workflow and text files as outcome when the --skip_quantification parameter is used

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
    • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
    • If necessary, also make a PR on the nf-core/mhcquant branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

nf-core-bot and others added 30 commits December 14, 2021 16:42
@nf-core-bot
Template update for nf-core/tools version 2.2
c91f07a
@jonasscheid
fix #184
c7afb0b
@marissaDubbelaar
Merge pull request #185 from jonasscheid/dev
03a7759 
Fix parsing for VEP annotated VCF files
@nf-core-bot
Template update for nf-core/tools version 2.3
0a30865
@SusiJo
Added reference links
c559d7b
@SusiJo
updated changelog
a20a654
@SusiJo
added issue # to changelog
6e78312
@SusiJo
fix markdown linting
75973c4
@WackerO
Updated parameter descriptions in nextflow_schema.json, set the defau…
d7061df 
…lt of run_centroidisation to false
@WackerO
Updated changelog
cb6af24
@SusiJo
Corrected format of samplesheet input in usage.md
f2fa4c4
@SusiJo
Merge branch 'nf-core:master' into samplesheet_format
3744d67
@WackerO
Updated parameter descriptions in nextflow_schema.json, set the defa…
4a5ddf5 
…ult of run_centroidisation to false, updated changelog
@WackerO
Merge branch 'param_docu' into params
784afe2
@SusiJo
Added backslashes to fix run command
6c9969d
@SusiJo
Merge branch 'nf-core:master' into run_command
eca4a18
@WackerO
Fixed conflict in changelog
c94320c
@SusiJo
Removed table of contents
4d95b9a
@marissaDubbelaar
Alteration of additional parameters
00945c7
@WackerO
Update nextflow_schema.json
ced5518
@WackerO
Fixed some typos
3005ea9
@WackerO
Updated Changelog
6208d2b
@marissaDubbelaar
Include repository type
cb2cd39
@marissaDubbelaar
Add end of line to .nf-core.yml
475d93b
@marissaDubbelaar
update template
3452e9e
@marissaDubbelaar
add new files
2ab924c
@marissaDubbelaar
add new files
d19490e
@marissaDubbelaar
Update template and nf-core modules
6f6b5a5
@marissaDubbelaar
correct linting
5c717cc
@marissaDubbelaar
add .yamllint.yml
ed68304
d4straub
d4straub reviewed Apr 4, 2022
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d4straub
d4straub reviewed Apr 4, 2022
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d4straub
d4straub reviewed Apr 4, 2022
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d4straub
d4straub reviewed Apr 4, 2022
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d4straub
d4straub reviewed Apr 4, 2022
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Looks good, except for the comments I made.

christopher-mohr
christopher-mohr approved these changes Apr 4, 2022
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LGTM! Only found some minor things.

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marissaDubbelaar and others added 19 commits April 4, 2022 17:30
@marissaDubbelaar
Merge with the nf-core template #208
a481a39
@marissaDubbelaar
Fix: prettier
daa53a7
@marissaDubbelaar
Remove: fastqc module
b919313
@marissaDubbelaar
Merge pull request #10 from marissaDubbelaar/template-update
d849bcd 
Template update
@marissaDubbelaar
Fix: ran agains upstream template branch and updated multiQC
f105246
@marissaDubbelaar
Fix: Prettier
03e8efc
@marissaDubbelaar
Merge pull request #11 from marissaDubbelaar/template-update
297acd4 
Template update
@marissaDubbelaar
Merge pull request #12 from marissaDubbelaar/dev
27eb21c 
Dev
@marissaDubbelaar
Fix: remove faulty template inclusions
a42da92
@marissaDubbelaar
Fix: resolve PR suggestions
54928de
@marissaDubbelaar
Merge pull request #13 from marissaDubbelaar/dev
7507ad9 
Fix: remove faulty template inclusions and include PR suggestions
@marissaDubbelaar
Alter: bump version to 2.3.0
2db54fa
@marissaDubbelaar
Merge pull request #14 from marissaDubbelaar/dev
e6b6335 
Alter: bump version to 2.3.0
@marissaDubbelaar
Include: depencancies in CHANGELOG
e1dbf51
@marissaDubbelaar
Merge pull request #15 from marissaDubbelaar/dev
3762874 
Include: dependancies in CHANGELOG
@marissaDubbelaar
Merge pull request #209 from marissaDubbelaar/master
6c4b3bb 
Supporting alteration for the template and PR suggestions
@marissaDubbelaar
Merge branch 'dev' into nf-core-template-merge-2.3.2
c7e5c9f
@marissaDubbelaar
Merge pull request #204 from nf-core/nf-core-template-merge-2.3.2
274ac82 
Important! Template update for nf-core/tools v2.3.2
@marissaDubbelaar @d4straub
Update .nf-core.yml
7fd13d0 
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
d4straub
d4straub approved these changes Apr 5, 2022
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Great!

@marissaDubbelaar marissaDubbelaar merged commit b24db1e into master Apr 5, 2022
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@christopher-mohr christopher-mohr christopher-mohr approved these changes

@d4straub d4straub d4straub approved these changes

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7 participants
@marissaDubbelaar @christopher-mohr @d4straub @nf-core-bot @jonasscheid @SusiJo @WackerO