Code

Update to DSL2 Best Practices#379

Code

Merged

maxulysse merged 53 commits intonf-core:dsl2nf-core/sarek:dsl2from maxulysse:dsl2_modules_updatemaxulysse/nf-core_sarek:dsl2_modules_updateCopy head branch name to clipboardJun 11, 2021

+4,908-3,987

Commits

Commits on May 20, 2021

• feat: update main script and lib from DSL2 Best Practices

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  1e0edf8

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• fix: add more file to lint ignore

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  b120e90

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• feat: strip out unused functions

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  b5fc96c

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• feat: update some modules

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  34a0b4d

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• fix: HaplotypeCaller

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Commits on May 25, 2021

• feat: update msisensor

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• feat: update msisensor_msi

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  f68fa78

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• fix: Gstring.toString()

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  b86fc4f

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• fix: output

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  7f55703

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• remove unused file

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• remove white space

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  6291ec5

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• fix: output

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Commits on May 26, 2021

• fix: markduplicates subworkflow test

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• fix: subworkflow md finally fixed

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• fix: nextflow version

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Commits on May 27, 2021

• moving files and functions around

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Commits on May 28, 2021

• feat: update modules and move around functions, and possibly break everything

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• fix: add .gitignore to .nf-core-lint.yml

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• fix: add new csv files

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• feat: simplify mapping script, update module, default test working

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  b83e31f

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• feat: cleanup files

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• cleanup

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• feat: simplify variant_calling

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Commits on May 30, 2021

• fix: output

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  6c3299d

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• feat: simplify tests

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• fix: tests

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Commits on Jun 3, 2021

• feat: simplify test profiles

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  7750ce9

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• feat: refactor + reorganize modules

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• feat: refactor - forgot to commit file

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Commits on Jun 4, 2021

• fix: gatk4/markduplicatesspark

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  7e6b232

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Commits on Jun 7, 2021

• fix: subworfklow tests

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• fix: markduplicats tests

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• feat: update bwa/bwamem2 modules

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• feat: update trimgalore

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  2b3b55c

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• feat: update tabix/tabix

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• feat: update and add strelka modules

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  7b2a7a3

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• fix: typo

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  61eee21

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• fix: path to module

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  b214c5d

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• fix: typo

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  0f1fba5

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• feat: update samtools/merge

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• feat: update multiqc modules

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• feat: replace msisensor by msisensor-pro

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  7dc1c86

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• fix: path to modules

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• fix: msisensor-pro test

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• fix: msisensorpro execution7

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  7d4547b

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• feat: code polishing

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  28b232b

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• fix: improve csv files generation

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  214a28b

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• feat: code polishing

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  6b23e8e

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• fix: update CI

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• fix: add csv for recalibrated bam files

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• feat: restart from all steps

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Commits on Jun 8, 2021

• fix: gatk4spark tests

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• feat: code polishing

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