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Exp/pathseq 20221024#6

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cschu wants to merge 15 commits intomainzellerlab/vortex_light:mainfrom exp/pathseq_20221024zellerlab/vortex_light:exp/pathseq_20221024Copy head branch name to clipboard

+1,493-369

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Commits on Oct 24, 2022

• made pathseq standalone

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  63c4950

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Commits on Oct 25, 2022

• Squashed 'nevermore/' changes from 37e095d..f07fbd0

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  42de1d0

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• Merge commit '42de1d023425bbb885e0646a9f5c8aaf5c7a666c' into exp/pathseq_20221024

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  7b87ba1

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• updated nvmlib incl. input procedures

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  e31e356

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• updated nvmlib incl. input procedures

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• added missing executables

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• corrected nevermore/bin symlinks

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  b284f6a

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• updated prepare_fastqs run configuration

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Commits on Oct 26, 2022

• added missing ExtractProfiledCounts script

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Commits on Jan 17, 2023

• update: add latest nvm structural changes to input and main workflow

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  e9f9e56

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• fix: added pathseq fix for 4.1.9+ versions

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• fix: parameter is called --microbe-dict not --microbe_dict

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• fix: use correct parameter for bam input

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Commits on May 29, 2024

• remove bin-symlinks for nf 23 compatibility

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• added collate_stats, v. 0.9

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