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Update diff subworkflows#7414

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suzannejin merged 20 commits intomasternf-core/modules:masterfrom update_diff_subworkflowsnf-core/modules:update_diff_subworkflowsCopy head branch name to clipboardFeb 13, 2025

+311-302

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Commits on Jan 31, 2025

• [gsea] unable default seed option

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• [subworkflow] update abundance_differential_filter to output a list of files for variance stabilised matrices. This is to facilitate the channel handling afterwards in the differentialabundance pip…

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• [gsea] add module test config

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• update functional subworkflow. Also update gprofiler2 related snapshots - as they changed after database update

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• [gprofiler2] add option to specify the database archive

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Commits on Feb 4, 2025

• [gsea] remove default seed set in gsea module

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• Merge branch 'master' into update_diff_subworkflows

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• change(abundance_differential_filter): use groupTuple for ch_variance_stabilised_matrix

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• change(differential and functional subworkflows): add back mergeMap and update snapshots

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• fix(snapshot): update gprofiler2/gost test snapshots

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Commits on Feb 5, 2025

• fix(gprofiler2_gost): set base url to an old archive for reproducibility.

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• Merge branch 'master' into update_diff_subworkflows

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Commits on Feb 6, 2025

• Merge branch 'master' into update_diff_subworkflows

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Commits on Feb 7, 2025

• fix(gprofiler2_gost): update test snapshots to match with the latest database

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• Merge branch 'master' into update_diff_subworkflows

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Commits on Feb 12, 2025

• simplify ch_variance_stabilised_matrix with groupTuple()

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• Merge branch 'master' into update_diff_subworkflows

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Commits on Feb 13, 2025

• update propd container

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• update differential and functional subworkflows by replacing 'method' by 'method_differential' and 'method_functional'

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• fix: update version snapshots for the new propd container

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