From a9f0a1e79104199e209e9295b66ef4d3f52f24db Mon Sep 17 00:00:00 2001 From: darrelln32 Date: Fri, 29 Mar 2024 11:15:42 -0400 Subject: [PATCH] Update cellranger.py updating versions of cellranger and spaceranger to have latest versions when 10X database is implemented --- scripts/cellranger.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/scripts/cellranger.py b/scripts/cellranger.py index cffe807..ca87b32 100644 --- a/scripts/cellranger.py +++ b/scripts/cellranger.py @@ -27,14 +27,14 @@ ACCESS = 0o775 config_dict = { "count": { - "tool": " /igo/work/nabors/tools/cellranger-7.0.0/cellranger count ", + "tool": " /igo/work/nabors/tools/cellranger-8.0.0/cellranger count ", "genome": { "Human": " --transcriptome=/igo/work/nabors/genomes/10X_Genomics/GEX/refdata-gex-GRCh38-2020-A ", "Mouse": " --transcriptome=/igo/work/nabors/genomes/10X_Genomics/GEX/refdata-gex-mm10-2020-A " } }, "vdj": { - "tool": " /igo/work/nabors/tools/cellranger-7.0.0/cellranger vdj ", + "tool": " /igo/work/nabors/tools/cellranger-8.0.0/cellranger vdj ", "genome": { "Human": " --reference=/igo/work/genomes/10X_Genomics/VDJ/refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0 ", "Mouse": " --reference=/igo/work/genomes/10X_Genomics/VDJ/refdata-cellranger-vdj-GRCm38-alts-ensembl-7.0.0 " @@ -55,17 +55,17 @@ } }, "multi": { - "tool": " /igo/work/nabors/tools/cellranger-7.0.0/cellranger multi " + "tool": " /igo/work/nabors/tools/cellranger-8.0.0/cellranger multi " }, "arc": { - "tool": " /igo/work/bin/cellranger-arc-2.0.0/cellranger-arc count ", + "tool": " /igo/work/bin/cellranger-arc-2.0.2/cellranger-arc count ", "genome": { "Human": " --reference=/igo/work/nabors/genomes/10X_Genomics/ARC/refdata-cellranger-arc-GRCh38-2020-A-2.0.0 ", "Mouse": " --reference=/igo/work/nabors/genomes/10X_Genomics/ARC/refdata-cellranger-arc-mm10-2020-A-2.0.0 " } }, "spaceranger": { - "tool": " /igo/work/nabors/tools/spaceranger-2.0.0/spaceranger count ", + "tool": " /igo/work/nabors/tools/spaceranger-3.0.0/spaceranger count ", "genome": { "Human": " --transcriptome=/igo/work/nabors/genomes/10X_Genomics/GEX/refdata-gex-GRCh38-2020-A ", "Mouse": " --transcriptome=/igo/work/nabors/genomes/10X_Genomics/spatial_gex/refdata-gex-mm10-2020-A " @@ -73,7 +73,7 @@ "probe": { "Human": "/igo/work/nabors/genomes/10X_Genomics/spatial_gex/Visium_Human_Transcriptome_Probe_Set_v1.0_GRCh38-2020-A.csv", "Human_CytAssist": "/igo/work/genomes/10X_Genomics/spaceranger/Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A.csv", - "Mouse": "/igo/work/nabors/tools/spaceranger-2.0.0/external/tenx_feature_references/targeted_panels/Visium_Mouse_Transcriptome_Probe_Set_v1.0_mm10-2020-A.csv" + "Mouse": "/igo/work/nabors/tools/spaceranger-3.0.0/external/tenx_feature_references/targeted_panels/Visium_Mouse_Transcriptome_Probe_Set_v1.0_mm10-2020-A.csv" } } }