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prep release 0.41.0#359

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dozy merged 31 commits intomasterwtsi-npg/p4:masterfrom develwtsi-npg/p4:develCopy head branch name to clipboardJan 31, 2025

+660-87

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Commits on Aug 29, 2024

• extend template preprocessing to subgraph_io sections (in subgraphs)

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• allow specification of input processing for stage2 analysis

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• allow selection of subsample methods (for QC)

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• alternate subsample methods

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• templates to support alternate input processing methods

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• static parameter files for stage2 reanalyses (initial set targetting NanoSeq)

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Commits on Sep 5, 2024

• set realignment_switch:0,pp_read2tags:on as as default in base_params_duplexseq param files

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Commits on Sep 6, 2024

• Merge pull request #349 from dozy/stage2_init_options

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Commits on Sep 13, 2024

• container: bump samtools/htslib to 1.21

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• CI: bump actions/upload-artifact to v3

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• Merge pull request #350 from dkj/samtools1.21

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Commits on Oct 1, 2024

• Added dependabot.yml to auto-update GitHub actions

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Commits on Oct 2, 2024

• Merge pull request #351 from avnishsinghh/dependabot

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• Bump actions/cache from 3 to 4

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• Bump actions/checkout from 3 to 4

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• Bump actions/upload-artifact from 3 to 4

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• Merge pull request #353 from wtsi-npg/dependabot/github_actions/actions/checkout-4

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• Merge pull request #352 from wtsi-npg/dependabot/github_actions/actions/cache-4

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• Merge pull request #354 from wtsi-npg/dependabot/github_actions/actions/upload-artifact-4

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Commits on Oct 11, 2024

• add static data for analyses:

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• downgrade bwa version to 0.7.17 (from 0.7.18) to match current DD production version of bwa

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Commits on Oct 14, 2024

• Merge pull request #355 from dozy/cont_analyses_static_data

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• add new P4 explainer README.md

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Commits on Oct 17, 2024

• add FASTQ input option to non-consented human split analysis

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Commits on Oct 18, 2024

• add static parameters file for container nchs reanalysis with FASTQ input

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• Merge pull request #356 from dkj/wtf

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Commits on Oct 22, 2024

• add dummy value for incrams parameter when using FASTQ input

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Commits on Oct 24, 2024

• Merge pull request #357 from dozy/nchs_fastq

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Commits on Jan 27, 2025

• documenting alternative ways of visualising

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Commits on Jan 28, 2025

• use the hash ascii code

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• Merge pull request #358 from jidur/doc_update

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