From 60fa337aa9ff08388dfbce602bd728ade69d64e7 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 19 Jul 2023 13:22:07 +0200 Subject: [PATCH 1/4] fix dim_red tsne --- .../dimensionality_reduction/methods/tsne/config.vsh.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml index 7ec1899577..0da62a6a83 100644 --- a/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml @@ -42,8 +42,8 @@ platforms: - cmake - gcc - type: python - packages: - - MulticoreTSNE + github: + - DmitryUlyanov/Multicore-TSNE - type: nextflow directives: label: [ highmem, highcpu ] From c52a86c2288e9fa604a8e07420e3cee6dec14a8c Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 20 Jul 2023 16:11:03 +0200 Subject: [PATCH 2/4] disable seurat_transferdata --- .../label_projection/methods/seurat_transferdata/config.vsh.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml b/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml index 50eef997cb..c8f5eadeb6 100644 --- a/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml +++ b/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml @@ -1,5 +1,6 @@ __merge__: ../../api/comp_method.yaml functionality: + status: disabled name: "seurat_transferdata" info: label: Seurat TransferData From e9a6b0c27a6233537856cb99c54cb76d69705c75 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 20 Jul 2023 16:16:41 +0200 Subject: [PATCH 3/4] update changelog --- CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 44625dad77..c5e1b60be6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,10 @@ * Update "baseline" to "control" (PR #146). +### BUG FIXES + +* fix dim_red and temp disbale label_projection test scripts (PR #206). + ## common ### NEW FUNCTIONALITY From 6a1139b5ce6a1d0b0ec08ef574897c2faada0c21 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Mon, 24 Jul 2023 10:42:58 +0200 Subject: [PATCH 4/4] Update CHANGELOG.md Co-authored-by: Robrecht Cannoodt --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c5e1b60be6..af546e7ef3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -20,7 +20,8 @@ ### BUG FIXES -* fix dim_red and temp disbale label_projection test scripts (PR #206). +* `dimensionality_reduction/methods/tsne`: Use GitHub version of MulticoreTSNE. +* `label_projection/methods/seurat_transferdata`: Temporarily disable component as it appears to not be working (PR #206). ## common