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Release v2.3.0 #666

Merged
merged 250 commits into from
Feb 13, 2025
Merged

Release v2.3.0 #666

merged 250 commits into from
Feb 13, 2025

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ramprasadn
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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/raredisease 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 --outdir <OUTDIR>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • 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).

ramprasadn and others added 30 commits September 13, 2024 13:58
@ramprasadn
add mito
3af2b52
@ramprasadn
annotate
a87672e
@ramprasadn
bumpversion
6dacbb6
@ramprasadn
align mt reads to mt and not genome
505c2b8
@ramprasadn
Merge pull request #610 from nf-core/bumpversion230
695ccc3 
Bumpversion 2.2.0->2.3.0dev
@ramprasadn
Merge branch 'dev' of github.com:nf-core/raredisease into mito
1a48be1
@ramprasadn
update changelog
9575a7f
@ramprasadn
include filter
2bb4586
@ramprasadn
update usage docs
537de87
@ramprasadn
prettier
099a566
@ramprasadn
update docs
a57f931
@ramprasadn
lint
877cb31
@ramprasadn
Merge pull request #608 from nf-core/mito
c3aacee 
Add option to analyse only mitochondria
@ramprasadn
Merge branch 'dev' of github.com:nf-core/raredisease into bcftools-fi…
eb963ec 
…lter
@ramprasadn
changelog
c1ddf4c
@ramprasadn
fix declaration error
7d5e14e
@jemten
allow vep 112
2a505df
@jemten
prettier
1021df2
@ramprasadn
update docs
69eb6a1
@ramprasadn
lint
931fc00
@ramprasadn
Merge pull request #616 from nf-core/bcftools-filter
df4db70 
5% frequency threshold for mitochondrial clinical vcfs
@ramprasadn
update README
d509436
@ramprasadn
Merge branch 'dev' of github.com:nf-core/raredisease into dev
39e473d
@ramprasadn
update module
953316b
@jemten
remove enum on vep cache version
5e177a2
@jemten
Merge branch 'dev' into add_vep_112_option
e583e15
@ramprasadn
Merge pull request #617 from nf-core/add_vep_112_option
985230b 
allow vep 112
@ramprasadn
Merge branch 'dev' into updatetabixbgzip
63f36cf
@ramprasadn
Merge pull request #618 from nf-core/updatetabixbgzip
7da78ba 
Minor fixes
@ramprasadn
update modules
64bea68
@danilodileo danilodileo self-requested a review February 12, 2025 08:23
fellen31
fellen31 reviewed Feb 12, 2025
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@fellen31 fellen31 left a comment

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Nice! Few comments.

conf/modules/align_sentieon.config Outdated Show resolved Hide resolved
conf/modules/prepare_references.config Outdated Show resolved Hide resolved
conf/modules/qc_bam.config Show resolved Hide resolved
docs/output.md Show resolved Hide resolved
ro-crate-metadata.json Show resolved Hide resolved
subworkflows/local/align_sentieon/main.nf Show resolved Hide resolved
subworkflows/local/prepare_references.nf Show resolved Hide resolved
workflows/raredisease.nf Show resolved Hide resolved
danilodileo
danilodileo approved these changes Feb 12, 2025
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Great job! Overall good, just a couple of comments:

  • on the folder structure in subworkflow/local. it's a bit inconsistent some subworkflows are inside folder, others are not. + I think the structure is subworkflows/local/name/function/main.nf
  • local modules and local subworkflows don't have meta.yml

These are not problematic at all in terms of pipeline functionality! But I am just pointing them out because of nf-core guidelines.

@ramprasadn ramprasadn requested a review from fellen31 February 12, 2025 12:32
@ramprasadn
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Great job! Overall good, just a couple of comments:

* on the folder structure in subworkflow/local. it's a bit inconsistent some subworkflows are inside folder, others are not. + I think the structure is subworkflows/local/name/function/main.nf

* local modules and local subworkflows don't have meta.yml

These are not problematic at all in terms of pipeline functionality! But I am just pointing them out because of nf-core guidelines.

Thanks, @danilodileo. Very valid points. I will try to address them in the next release.

maxulysse
maxulysse reviewed Feb 12, 2025
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ro-crate-metadata.json
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I assume you updated the README since this file was generated.
Can you regenerate that file using nf-core/tools?

maxulysse
maxulysse reviewed Feb 12, 2025
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Looking good to me.
I think the RO crate can be re-generated, but to be honest, it's easy to miss as tools does not regenerate it by default.

@ramprasadn ramprasadn merged commit fe9f0ad into master Feb 13, 2025
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@maxulysse maxulysse maxulysse left review comments

@rannick rannick rannick approved these changes

@fellen31 fellen31 fellen31 approved these changes

@danilodileo danilodileo danilodileo approved these changes

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9 participants
@ramprasadn @rannick @maxulysse @fellen31 @danilodileo @jemten @nf-core-bot @peterpru @fevac