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CHORES: update all modules#1304

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maxulysse merged 21 commits intonf-core:devnf-core/sarek:devfrom maxulysse:modulesmaxulysse/nf-core_sarek:modulesCopy head branch name to clipboardNov 3, 2023

+3,088-632

Commits

Commits on Nov 1, 2023

• update all modules (will probably break things)

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  9d15b23

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• simpler patch for bcftools-annotate

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  bc1b3bd

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• finish proper patching of bcftools/annotate

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  795c2a5

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• restore patch for controlfreec/assesssignificance

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  49b55bd

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• restore patch for dragmap/hashtable

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  b7b0720

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• update CHANGELOG

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  7bae363

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• update CHANGELOG

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  994a84a

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• fix bcfann tests

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  1021445

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• fix channels for bcftools/mpileup

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  c00d630

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• fix channels for cnvkit/batch

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  78f311a

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• fix channels for manta

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  2f0747a

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• if the vcf.gz changes on rerun, pretty sure the vcf.gz.tbi does the same

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  cccc364

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• no need for --download_cache here

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  6cf72f4

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Commits on Nov 2, 2023

• update gatk4spark modules and subworkflows

  maxulysse

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  a60b744

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• Update subworkflows/local/bam_applybqsr_spark/main.nf

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  72a45b9

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• update base.config

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  1501fa4

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• add info about changed names

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  f8ecd4e

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• rename tag to gatk4spark

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  745e415

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Commits on Nov 3, 2023

• fix config

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  202ebd9

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• '' ->

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  63348f7

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• exclude failing nf-tests due to missing data from modules

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  8b1b2e9

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