Fixed Conda dependency issues in environment.yml#211

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KurayiChawatama wants to merge 26 commits intonf-core:devfrom

KurayiChawatama:fix/conda-improvements

Commits on Aug 19, 2025

changed base.config process_medium settings for local runs
KurayiChawatama
committed
fixed conda profile highly_variable column not boolean error
KurayiChawatama
committed
added missing singlecellexperiment and r2py libs to environment.yml
KurayiChawatama
committed
fixed rpy2 version fetch crash
KurayiChawatama
committed
fixed upset plot script python fetch fail crash
KurayiChawatama
committed
added missing libs to doublet removal env yml
KurayiChawatama
committed
fixed doublet removal script python fetch fail crash
KurayiChawatama
committed
added evironment yml to scds to allow conda based running
KurayiChawatama
committed
updated liana env yml to include missing conda packadges
KurayiChawatama
committed
added missing scrublet lib to env yml
KurayiChawatama
committed
added missing libs to doublet detection env yml
KurayiChawatama
committed
added missing libs to solo env yml
KurayiChawatama
committed
untested attempted addition of SingleR support to the pipeline
KurayiChawatama
committed
Revert "untested attempted addition of SingleR support to the pipeline"
KurayiChawatama
committed
reset base.config to it's original state
KurayiChawatama
committed
reset the scds module to it's original condaless state
KurayiChawatama
committed
added correct conda dependencies for liana rankaggregate to run
KurayiChawatama
committed
reset liana rankagreggate env to it's original state
KurayiChawatama
committed
reverted nf-core solo env.yml to original state
KurayiChawatama
committed
restored nf-core doubletdetection env.yml to original version
KurayiChawatama
committed
Fix: Sync logo to match nf-core template (lint fix)
KurayiChawatama
committed
resolved the issues raised in the PR
KurayiChawatama
committed
added the container images to match env yaml changes, removed changes to nf-core modules
KurayiChawatama
committed
matched liana py to upstream, removed scrublet environment yaml
KurayiChawatama
committed

Commits on Aug 20, 2025

fix(doublet_removal): update environment to NumPy 2–compatible stack
KurayiChawatama
committed
updated doublet removal contianers to match changes to env yml
KurayiChawatama
committed

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Fixed Conda dependency issues in environment.yml#211

Fixed Conda dependency issues in environment.yml#211
KurayiChawatama wants to merge 26 commits intonf-core:devfrom
KurayiChawatama:fix/conda-improvements

Commits on Aug 19, 2025

changed base.config process_medium settings for local runs

fixed conda profile highly_variable column not boolean error

added missing singlecellexperiment and r2py libs to environment.yml

fixed rpy2 version fetch crash

fixed upset plot script python fetch fail crash

added missing libs to doublet removal env yml

fixed doublet removal script python fetch fail crash

added evironment yml to scds to allow conda based running

updated liana env yml to include missing conda packadges

added missing scrublet lib to env yml

added missing libs to doublet detection env yml

added missing libs to solo env yml

untested attempted addition of SingleR support to the pipeline

Revert "untested attempted addition of SingleR support to the pipeline"

reset base.config to it's original state

reset the scds module to it's original condaless state

added correct conda dependencies for liana rankaggregate to run

reset liana rankagreggate env to it's original state

reverted nf-core solo env.yml to original state

restored nf-core doubletdetection env.yml to original version

Fix: Sync logo to match nf-core template (lint fix)

resolved the issues raised in the PR

added the container images to match env yaml changes, removed changes to nf-core modules

matched liana py to upstream, removed scrublet environment yaml

Commits on Aug 20, 2025

fix(doublet_removal): update environment to NumPy 2–compatible stack

updated doublet removal contianers to match changes to env yml