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Release candidate 3.2.2 #1096

Merged
merged 69 commits into from
Jun 15, 2023
Merged

Release candidate 3.2.2 #1096

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e79b306
FIX: gatk4/createsequencedictionary default memory
maxulysse Jun 9, 2023
7cf95fe
update CHANGELOG
maxulysse Jun 9, 2023
ecf8e72
remove md5checksum
maxulysse Jun 9, 2023
5c2017d
Merge pull request #1087 from maxulysse/new_dev
maxulysse Jun 9, 2023
01119fe
replace test by test_cache and add test with non obfuscated files
maxulysse Jun 9, 2023
641cdbc
Merge branch 'dev' into test_cache
maxulysse Jun 9, 2023
ab8ced4
update CHANGELOG
maxulysse Jun 9, 2023
162ac72
test only on docker
maxulysse Jun 9, 2023
1f40c3d
test with singularity and conda when PR on master
maxulysse Jun 9, 2023
51a3ede
Apply suggestions from code review
maxulysse Jun 9, 2023
c19188e
Update .github/workflows/pytest-workflow_release.yml
maxulysse Jun 9, 2023
4d0a5f3
update usage
maxulysse Jun 9, 2023
67c1186
Merge branch 'test_cache' of github.com:maxulysse/nf-core_sarek into …
maxulysse Jun 9, 2023
51ac097
remove duplicated code
maxulysse Jun 9, 2023
3a4a7f8
update CHANGELOG
maxulysse Jun 9, 2023
7fcf0fc
update CHANGELOG
maxulysse Jun 9, 2023
bce4a4c
Merge pull request #1089 from maxulysse/duplication
maxulysse Jun 9, 2023
5c45e5c
Merge pull request #1088 from maxulysse/test_cache
maxulysse Jun 9, 2023
7b10235
Reverting meta.id in channels allele_files, loci_files, gc_file and r…
asp8200 Jun 9, 2023
f238efa
Merge branch 'dev' into fix_ascat_manual_test
asp8200 Jun 9, 2023
c3eb660
Updating changelog
asp8200 Jun 9, 2023
ecb49a8
Merge pull request #1093 from nf-core/fix_ascat_manual_test
maxulysse Jun 9, 2023
fbe6059
prepare 3.2.2
maxulysse Jun 12, 2023
f5389b6
Update CHANGELOG.md
maxulysse Jun 12, 2023
3dce752
Merge pull request #1095 from maxulysse/prepare_release-3.2.2
maxulysse Jun 12, 2023
b9030ff
fix Mutect2 subworkflow bug
maxulysse Jun 12, 2023
15909a4
remove duplicate index for deepvariant when no_intervals
maxulysse Jun 12, 2023
66ce8e8
update CHANGELOG
maxulysse Jun 12, 2023
400b4ae
Merge pull request #1098 from maxulysse/fix_mutect2_subworkflow
maxulysse Jun 12, 2023
693028e
Merge branch 'dev' into deepvariant_intervals
maxulysse Jun 12, 2023
1a9328a
Merge pull request #1100 from maxulysse/deepvariant_intervals
maxulysse Jun 12, 2023
c9eaba9
remove redundant index computation [skip ci]
FriederikeHanssen Jun 12, 2023
9c3cc8b
update changelog [skip ci]
FriederikeHanssen Jun 12, 2023
0bba02c
remove params.tracedir
maxulysse Jun 13, 2023
ee6e461
Merge pull request #1105 from maxulysse/remove_tracedir
maxulysse Jun 13, 2023
3215fe4
add Slack integration
maxulysse Jun 13, 2023
a803e27
it's a params
maxulysse Jun 13, 2023
c42f0b4
Merge pull request #1106 from maxulysse/remove_tracedir
maxulysse Jun 13, 2023
ac63797
update md modules
FriederikeHanssen Jun 14, 2023
72d6026
Merge branch 'dev' into issue_1065
FriederikeHanssen Jun 14, 2023
401cf54
Revert wrong checksum change
FriederikeHanssen Jun 14, 2023
07a4d5f
[automated] Fix linting with Prettier
nf-core-bot Jun 14, 2023
8be49d9
remove unnecessary import
FriederikeHanssen Jun 14, 2023
8306a79
Merge pull request #1101 from FriederikeHanssen/issue_1065
maxulysse Jun 14, 2023
c940aca
update config
maxulysse Jun 14, 2023
9c350a8
Merge branch 'dev' into public_aws_ecr_singularity
maxulysse Jun 14, 2023
6ead4a9
update CHANGELOG
maxulysse Jun 14, 2023
875faee
Merge pull request #1107 from maxulysse/public_aws_ecr_singularity
maxulysse Jun 14, 2023
91c8c89
refactor prefix definition for vcf files
maxulysse Jun 14, 2023
806f3d6
baseName, not name
maxulysse Jun 14, 2023
febf7d8
Update conf/modules/joint_germline.config
maxulysse Jun 14, 2023
6276707
variant_file not vcf
maxulysse Jun 14, 2023
abc7fe6
Merge pull request #1108 from maxulysse/remove_minus
maxulysse Jun 14, 2023
37be36d
fix bcftools mpileup
FriederikeHanssen Jun 15, 2023
59923eb
consolidate docs
FriederikeHanssen Jun 15, 2023
5213603
Update changelog
FriederikeHanssen Jun 15, 2023
f31d7e0
Merge branch 'dev' into mpileup
maxulysse Jun 15, 2023
387f4f4
also fix annotation for mpileup
FriederikeHanssen Jun 15, 2023
b7b1655
Merge remote-tracking branch 'origin/mpileup' into mpileup
FriederikeHanssen Jun 15, 2023
0ed285e
Update subworkflows/local/bam_variant_calling_mpileup/main.nf
FriederikeHanssen Jun 15, 2023
4345074
Update subworkflows/local/bam_variant_calling_tumor_only_all/main.nf
FriederikeHanssen Jun 15, 2023
62aa7ee
Update .github/workflows/pytest-workflow_release.yml
maxulysse Jun 15, 2023
fcd5b64
fix more publishing issues with mpileup
FriederikeHanssen Jun 15, 2023
c190e9e
Merge remote-tracking branch 'origin/mpileup' into mpileup
FriederikeHanssen Jun 15, 2023
e3d80cf
Update tests/test_mpileup.yml
FriederikeHanssen Jun 15, 2023
8fb0b53
variable md5sums
FriederikeHanssen Jun 15, 2023
2e2397d
Update tests/test_mpileup.yml
FriederikeHanssen Jun 15, 2023
8e5bb2d
Merge pull request #1109 from FriederikeHanssen/mpileup
FriederikeHanssen Jun 15, 2023
702e3bc
Apply suggestions from code review
maxulysse Jun 15, 2023
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remove md5checksum
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@maxulysse
maxulysse committed Jun 9, 2023
commit ecf8e727042a08a5d8b1e6cad657e38f0f67225d
8 changes: 4 additions & 4 deletions tests/test_joint_germline.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -13,13 +13,13 @@
- path: results/preprocessing/recalibrated/test/test.recal.cram.crai
should_exist: false
- path: results/reports/bcftools/haplotypecaller/joint_variant_calling/joint_germline.bcftools_stats.txt
md5sum: 404d1208df301a6726f5543245625ef3
# Not stable enough
- path: results/reports/vcftools/haplotypecaller/joint_variant_calling/joint_germline.FILTER.summary
md5sum: 87a84b5f8ac3d3cbeeef7d60afcdbfe7
# Not stable enough
- path: results/reports/vcftools/haplotypecaller/joint_variant_calling/joint_germline.TsTv.count
md5sum: 974f6922981c87bb017b124aa009f654
# Not stable enough
- path: results/reports/vcftools/haplotypecaller/joint_variant_calling/joint_germline.TsTv.qual
md5sum: 1e34357e5848c318f8c2c7d3b041d229
# Not stable enough
- path: results/variant_calling/haplotypecaller/joint_variant_calling/joint_germline.vcf.gz
# binary changes md5sums on reruns
- path: results/variant_calling/haplotypecaller/joint_variant_calling/joint_germline.vcf.gz.tbi
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