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Integrate subworkflows into pipeline#431

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suzannejin wants to merge 31 commits intodevnf-core/differentialabundance:devfrom integrate_subworkflowsnf-core/differentialabundance:integrate_subworkflowsCopy head branch name to clipboard

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Commits on Jan 27, 2025

• Squashed commit of the following:

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• Revert squashed commit of dev-ratio to updated dev code.

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• installed subworkflows and associated modules

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• update modules

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• update workflow to use the updated modules. It runs through test profile, but still need to check nf-test

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Commits on Jan 29, 2025

• [abundance_differential_filter] separate channels for rlog and vst

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• [subworkflows] remove mergeMaps. Otherwise the contrastid_expid format of output file names lead to error at rmarkdown step.

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• update modules.config

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• [workflow] a first version that calls the subworkflows and properly runs till the end. Still need to pass nf-test

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• fix pre-commit

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• [module] revert gsea seed to its previous behaviour. This will pass the default pipeline test

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• update test.snap

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• [workflow] set ch_gene_sets and ch_background to Channel.of([[]]) when not provided

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Commits on Jan 30, 2025

• [pipeline] update modules.config to add LIMMA_NORM config, when using limma voom for rnaseq.

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• update test_rnaseq_limma snapshot

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• merge from dev - after new yaml contrast logic is introduced

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• [bug] update workflow to properly handle ch_norm

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• update test snapshots

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• [test] update test snapshots - from singularity to docker

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• Merge pull request #430 from suzannejin/dev-ratio-new

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Commits on Jan 31, 2025

• [modules] revert deseq2 modules into the version originally installed in the pipeline - to avoid test snapshots inconsistencies related to decimal handling

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• [feature] update differential subworkflow and pipeline for a common variance_stabilised_matrix channel. Also fixed the code in the pipeline to properly handle it

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• update changelog

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Commits on Feb 4, 2025

• remove subset option from LIMMA_NORM and DESEQ2_NORM

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• change(differentialabundance): simplify tools_differential and tools_functional declaration.

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• change(differentialabundance): use map criterias instead of meta method replacement function

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• change(abundance_differential_filter): use groupTuple for ch_variance_stabilised_matrix

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• change(subworkflows and report): revert to mergeMaps in differential and functional subworkflows. Also fix issues encountered in rmarkdown file. And update test snapshots

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• change(tests): ignore pngs from test snapshotting

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• fix(tests): remove unstable files from affy test snapshots

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• fix(tests): remove redundant ignore png

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