From 9273bc547ae6b67f1df12bdb4339100f1c7cbcac Mon Sep 17 00:00:00 2001 From: Wojciech Lason <40389067+wlason@users.noreply.github.com> Date: Thu, 25 Jul 2024 11:23:30 +0100 Subject: [PATCH 1/2] Update integration yaml - Added column_continuous argument to yaml with no value so that ruffus correctly interprets it as None - Changed default ATAC dimred to LSI --- panpipes/panpipes/pipeline_integration/pipeline.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/panpipes/panpipes/pipeline_integration/pipeline.yml b/panpipes/panpipes/pipeline_integration/pipeline.yml index 354e5f2c..07fbdfa6 100644 --- a/panpipes/panpipes/pipeline_integration/pipeline.yml +++ b/panpipes/panpipes/pipeline_integration/pipeline.yml @@ -113,7 +113,7 @@ prot: # ATAC modality atac: run: False - dimred: PCA + dimred: LSI tools: column: sample_id @@ -146,7 +146,8 @@ multimodal: - WNN - totalvi - multiVI - column_categorical: sample_id + column_categorical: sample_id + column_continuous: # TotalVI arguments totalvi: From e2a8e40fcf83af563b738f173d21f1e1f266a00c Mon Sep 17 00:00:00 2001 From: bio-la Date: Wed, 4 Sep 2024 11:25:41 +0200 Subject: [PATCH 2/2] updated branch --- panpipes/panpipes/pipeline_integration/pipeline.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/panpipes/panpipes/pipeline_integration/pipeline.yml b/panpipes/panpipes/pipeline_integration/pipeline.yml index 8b52ff82..41b3f1d5 100644 --- a/panpipes/panpipes/pipeline_integration/pipeline.yml +++ b/panpipes/panpipes/pipeline_integration/pipeline.yml @@ -113,7 +113,7 @@ prot: # ATAC modality atac: run: False - dimred: LSI + dimred: PCA tools: column: sample_id