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Dsl2 new test configs#1121

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TCLamnidis merged 67 commits intonf-core:devnf-core/eager:devfrom

jbv2:dsl2-new_test_configsjbv2/eager:dsl2-new_test_configsCopy head branch name to clipboard

May 2, 2025

Commits

Commits on Feb 28, 2025

• adding modern test

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• adding microbial genome test, but missing samplesheet dsl2 to test

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Commits on Mar 7, 2025

• adding short dna, still need the ncbi dir to be set

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• adding test_humanpopgen

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• adding test default

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• minor updates

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Commits on Mar 14, 2025

• finnished v1 test configs

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• finnished but error with mapDamage --rescale. Mixing different references

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Commits on Mar 24, 2025

• removing old profiles

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• replacing test.config

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• replacing nothing to minimal

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• adding genotyping source

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• update nextflow.config

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Commits on Mar 25, 2025

• Merge branch 'dev' into dsl2-new_test_configs

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• Update conf/test.config

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• Update conf/test.config

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• Move kraken2 to humanpopgen

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• removing fastp

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• adding fastp and changing input and fasta

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• excluding fasta

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• Deactivate rescaling, fix freebayes problem

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• Merge branch 'dsl2-new_test_configs' of https://github.com/jbv2/eager into dsl2-new_test_configs

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Commits on Mar 26, 2025

• Merge branch 'dev' into dsl2-new_test_configs

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Commits on Mar 28, 2025

• Update conf/modules.config

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• Update conf/modules.config

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• Merge branch 'dev' into dsl2-new_test_configs

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• Update conf/modules.config

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• And for haplotypecaller

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• Merge branch 'dsl2-new_test_configs' of https://github.com/jbv2/eager into dsl2-new_test_configs

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Commits on Apr 4, 2025

• Use correct GATK UG ploidy flag and remove duplicate

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• Use new test configs in ci test

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• Fix parameter for GATK HC too

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• Replace minimal test data with mammoth mt data to run faster

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• Fix HC caller command as they renamed the parameter

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• Limit MALT memory

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Commits on Apr 11, 2025

• removing double test profiles

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• adding missing rescale step

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• not rescaling

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• add test_long.config

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• final rev

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• changing mapping tool

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• getting manipulate damage from eager/dev

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• getting manipulate damage from eager/dev

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• increasing time for test long

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• Merge branch 'dev' into dsl2-new_test_configs

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Commits on Apr 25, 2025

• fixing problem with merging mapad

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• updating short_dna to run map AD

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• removing params from CI

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• latest_everything

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• changing input to run mapad

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• adding rescaled as source for genotyping

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• swap to fastp

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• add adapterlist

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• specifying elongation factor

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• fix typo

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• add mapdamage downsampling

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• Merge branch 'dsl2-new_test_configs' of https://github.com/jbv2/eager into dsl2-new_test_configs

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• Merge branch 'dsl2-new_test_configs' of https://github.com/jbv2/eager into dsl2-new_test_configs

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• fix profile names in commented commands

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• Update .github/workflows/ci.yml

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• Revert "swap to fastp"

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• swap to adapterremoval

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• add snpcapturebed

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Commits on May 2, 2025

• move java opts to beforescript

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• Merge branch 'dev' into dsl2-new_test_configs

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• re-add latest-everything

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• Update subworkflows/local/genotype.nf

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