Improve celltype-specific rankgenesgroups implementation#217

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nictru wants to merge 15 commits intodevfrom

212-make-rankgenesgroups-be-aware-of-cell-types

Commits on Jan 10, 2026

Simplify per-group subworkflow interface
nictru
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add differential expression subworkflow

an-altosian
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nictru
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for each comparison group, do DE for each other group and the rest

an-altosian
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nictru
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remove intermediate files

an-altosian
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nictru
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switch to wilcoxon for DE

an-altosian
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nictru
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work on DE result folder

an-altosian
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nictru
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add method arg for DE method selection

an-altosian
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nictru
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expose rangenegroups_method as a parameter

an-altosian
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nictru
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write json files for DE results; expose sample_group_col and method parameters

an-altosian
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nictru
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write json files for DE results; expose sample_group_col and method parameters

an-altosian
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nictru
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emit the outdir

an-altosian
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nictru
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emit the outdir of DE analysis

an-altosian
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nictru
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Remove trailing whitespace
nictru
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Add differential expression options to nextflow schema properly
nictru
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Fix EOF issues
nictru
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