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Release v1.9.0#239

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nvnieuwk merged 200 commits intomainnf-cmgg/germline:mainfrom devnf-cmgg/germline:devCopy head branch name to clipboardJan 9, 2025

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Commits on Sep 30, 2024

• back to dev

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Commits on Oct 1, 2024

• fix WES validation

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• add --squash-ploidy to vcfeval

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• fix vcfanno input

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• fix vardict flow

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• move some index creation around

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Commits on Oct 7, 2024

• fix WGS updio

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• add a --min_callable_coverage parameter

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• update changelog

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Commits on Oct 8, 2024

• fix bcftools filter

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• bump ci back to stable nf-core

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• small typo in the actions

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• fix vardict snap

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Commits on Oct 10, 2024

• Merge pull request #204 from nf-cmgg/fix-WES-validation

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• update docs

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• add skip features to nf-core.yml

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• pre-commit

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Commits on Oct 11, 2024

• make nf-core lint happy

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• Merge pull request #206 from nf-cmgg/template-v3.0.1

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• bump all modules

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Commits on Oct 14, 2024

• update subwfs part 1

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• fix annotation subwf tests

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Commits on Oct 18, 2024

• template 3.0.1

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• fix some syntax in nf-core modules

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Commits on Oct 21, 2024

• update annotation subwf

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• Merge pull request #210 from nf-cmgg/ben-made-me-do-more

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Commits on Oct 23, 2024

• move bam conversion to cram_prepare_samtools_bedtools

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• separate dbnsp annotation from vardictjava subwf

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• move filtering to the main wf

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• move genotyping out of the gatk4 subwf

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• add elprep

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• fix some small issues

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Commits on Oct 24, 2024

• correct channels

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• fix dbsnp subwf

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• fix dbsnp flow issue

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• fix wrong map + resources

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• small memory fix

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• module -> process in ci

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• add test for bam_call_elprep

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Commits on Nov 5, 2024

• fix some more tests

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• more test fixes

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• fix elprep/filter test

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• fix linting + reimplement only_call and only_merge

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• add some out channels as preparation for the new output definitions

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Commits on Nov 6, 2024

• migrate to new workflow output definitions

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Commits on Nov 7, 2024

• readd some missing pipeline outputs

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• new output structure

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Commits on Nov 12, 2024

• Merge pull request #212 from nf-cmgg/new-flow-elprep

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• Fix some resources (#220)

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• Merge branch 'dev' into output-defs

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Commits on Nov 13, 2024

• fix resource usage and patch modules

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• Merge branch 'dev' into output-defs

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• vcf2db: restore ext.args

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• Merge pull request #221 from nf-cmgg/fix/typo

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• fix tests

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• fix linting

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• fix genomes in summary

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• fix utils_nextflow_pipeline

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• test filter_beds

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Commits on Nov 14, 2024

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• test updio and merge_beds

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• move subwf tests to the subwf folder

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• add restrictions on sample and family name

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• update rtgtools/format

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• Merge branch 'nf-test-local-modules' into nf-test-local-subworkflows

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• test vcf_concat_bcftools

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• test vcf_filter_bcftools

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• add a test coverage ci comment

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• pre-commit

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• print out the coverage in the ci logs

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• fix missing $ in coverage action

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• update shell

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• try another method

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• use env instead

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• use another env method

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• use another env method

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• try even more methods

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• convert points to -

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• fix wrongly place quote

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• run all tests on PRs to main

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• fix if statement

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• fix test vcf_ped_rtgtools + fix ci

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• fix cram prepare subwf tests

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• fix more workflow tests

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• set test dir to root of repo

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• don't do disk space cleanup anymore

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Commits on Nov 18, 2024

• first changes

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• update output docs

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• update the docs some more

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Commits on Nov 19, 2024

• lower all gatk4 resources

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• Merge pull request #225 from nf-cmgg/fix/gatk4-resources

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• Merge pull request #222 from nf-cmgg/new-output-dir

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• bump vcf2db

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• Merge pull request #223 from nf-cmgg/nf-test-local-modules

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• update metro map + changelog

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• fix tests

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• more metro map updates

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• Merge pull request #226 from nf-cmgg/bump/vcf2db

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• prettier

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Commits on Nov 20, 2024

• detect HOOK_URL from env

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• Merge pull request #228 from nf-cmgg/fix/hook-url

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• replace dots with underscores

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• Merge pull request #230 from nf-cmgg/fix-broken-family-names

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• final small tweaks to the metro map

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• Merge branch 'dev' into docs-update

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• Merge pull request #227 from nf-cmgg/docs-update

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• fix build docs

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• Merge pull request #231 from nf-cmgg/fix-docs-build

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• try to fix docs building

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• try to fix docs building again

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• try to fix docs building again

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• try to fix docs building again again

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• do a deep dive in broken docs ci

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• finally fixed?

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• fix mosdepth test

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Commits on Nov 22, 2024

• set genotypegvcfs to process_single

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• add some new custom profiles (#229)

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• fix typo

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Commits on Nov 25, 2024

• Merge pull request #232 from nf-cmgg/lower-gatk-resources-more

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• fix output over multiple days

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• Merge pull request #234 from nf-cmgg/fix-output-definitions-for-long-runs

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• fix only_call and only_merge (#235)

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• fix family name issues

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• Merge pull request #236 from nf-cmgg/fix-family-name

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• fix prepare join issue (#238)

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Commits on Nov 26, 2024

• bump to 1.9.0

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• try to fix CI

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• try to fix CI

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• fix version in nf-core.yml

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• add somalier reports to multiqc output

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• update changelog

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• fix build-docs issue

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• Merge pull request #240 from nf-cmgg/multiqc-test-somalier

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• Remove output suffix param (#243)

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• add multiqc_data to output (#242)

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• restore default mem for VEP

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• update profiles

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• Merge pull request #245 from nf-cmgg/fix/VEP_mem

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• remove maxentscan from seqplorer config

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• Merge pull request #246 from nf-cmgg/update-profiles

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• force tabix to overwrite

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• Merge pull request #247 from nf-cmgg/fix/force_tabix

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• add updio and automap to wes profile (#248)

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• update vcf2db

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• Fix config to let the tests run correctly

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• Merge pull request #249 from nf-cmgg/update-vcf2db

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• set vcf32db to process_single

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• add date to changelog

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