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Release 1.2.0 #165

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Release 1.2.0 #165

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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/rnavar 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>).
  • 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).

maxulysse and others added 30 commits February 1, 2024 13:49
@maxulysse
Merge branch 'dev' into nf-core-template-merge-2.12
18726fe
@maxulysse
fix schema
ce95d67
@maxulysse
template logo
c226ebe
@maxulysse
update .editorconfig
06d30fe
@maxulysse
prettier
ccce756
@maxulysse
editor config
9f45743
@maxulysse
logo from template
ca46c28
@maxulysse
Merge pull request #120 from nf-core/nf-core-template-merge-2.12
ebb949b 
Important! Template update for nf-core/tools v2.12
@nschcolnicov
Fixed S3 bucket path in conditional statements
e5493bb
@nschcolnicov
Updated Changelog
557d23f
@nf-core-bot
[automated] Fix linting with Prettier
a42bb7e
@maxulysse
Merge pull request #124 from nschcolnicov/dev
dc05d53 
Fixed S3 bucket path in conditional statements
@maxulysse
Merge pull request #106 from nf-core/bounlu-patch-2
0429e57 
fix vep_cache
@nschcolnicov
Fixed VEP s3 bucket path
111e322
@nschcolnicov
Updated changelog with PR
3de9b74
@maxulysse
Merge pull request #127 from nschcolnicov/fix_vep
d47e3ff 
Fixed VEP s3 bucket path
@nschcolnicov
Added missing defs
36755fe
@nschcolnicov
Modified Changelog
1462823
@nschcolnicov
Updated readme
7a3bef9
@nschcolnicov @maxulysse
Update CHANGELOG.md
80f755c 
Co-authored-by: Maxime U Garcia <[email protected]>
@nf-core-bot
Template update for nf-core/tools version 2.13
37282c4
@maxulysse
Merge pull request #130 from nschcolnicov/fix_multi_sample
9036f17 
Added missing defs
@nschcolnicov
Fixed null value in publish dir
f22ec03
@maxulysse
Merge pull request #132 from nschcolnicov/fix_publish_dir
07dee64 
Fixed null value in publish dir
@nf-core-bot
Template update for nf-core/tools version 2.13.1
a31daa6
@nschcolnicov
Replaced UNZIP with GUNZIP
83fef7b
@nschcolnicov
Updated changelog, removed unnecesary module, not in use
4438535
@maxulysse
Merge pull request #136 from nschcolnicov/fix_unzip
45c2b2a 
Replaced UNZIP with GUNZIP
@MathieuCharlesINRAE
Modification for indexation on gvcf
02d4825
@maxulysse
Merge branch 'dev' into gvcf
62e673d
maxulysse and others added 30 commits March 4, 2025 11:07
@maxulysse
WIP
d48306b
@maxulysse
keep config the same
379e79c
@maxulysse
properly ignore tests
3c338d5
@maxulysse
properly ignore tests
d956911
@maxulysse
Merge pull request #178 from maxulysse/nf-test-automatic-shard
0d3cd0f 
implement automatic sharding for nf-test
@nvnieuwk
update README
9173ddc
@nvnieuwk
Merge branch 'dev' into docs
d93caff
@nvnieuwk
remove unused file
0343d5a
@nvnieuwk
update citations
23e3aff
@nvnieuwk
update usage docs
a85e4cc
@nvnieuwk
update output docs
8a4dbde
@nvnieuwk
changelog
afa81dd
@nvnieuwk @maxulysse
Update CITATIONS.md
ad4db75 
Co-authored-by: Maxime U Garcia <[email protected]>
@nvnieuwk
add nvnieuwk to nextflow.config
e9297af
@nvnieuwk
add vcf_annotate_all tests
db4410b
@nvnieuwk
remove comments
006610f
@nvnieuwk
add splitncigar tests
bbd2eca
@nvnieuwk
test recalibrate
99ef03a
@nvnieuwk
test prepare_genome
47c0f42
@nvnieuwk
test prepare_alignment
6ea6d5f
@nvnieuwk
test cram_qc_mosdepth_samtools
62f742c
@nvnieuwk
test gtf2bed
c0778fc
@nvnieuwk
test remove_unknown_regions
a34755e
@nvnieuwk
changelog
e04af45
@nvnieuwk
correctly run tests
69f190f
@nvnieuwk
update snpeff/snpeff
b469d13
@maxulysse
Merge pull request #187 from nvnieuwk/add/more-tests
6560d67 
Add unit tests for local subworkflows and processes
@maxulysse
Merge pull request #185 from nvnieuwk/docs
24828c1 
Update docs and README
@nvnieuwk
fix issue with star index being queue channel
56bd9df
@maxulysse
Merge pull request #190 from nvnieuwk/fix/multiple-fastqs
de8326d 
Fix issue with star index being queue channel
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7 participants
@maxulysse @nschcolnicov @nf-core-bot @MathieuCharlesINRAE @robsyme @fmalmeida @nvnieuwk