Merge branch 'master' into carla_time

cribbslab · Feb 1, 2024 · 8febc98 · 8febc98
2 parents 1510a14 + 0f67660
commit 8febc98
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Showing 4 changed files with 9 additions and 4 deletions.
diff --git a/conda/environments/scflow.yml b/conda/environments/scflow.yml
@@ -42,5 +42,8 @@ dependencies:
  - bioconductor-scdblfinder
  - bioconductor-singlecellexperiment
  - bioconductor-biomart
+ - bioconductor-scuttle
+ - bioconductor-glmgampoi
  - r-harmony
  - r-seuratdisk
+ - r-clustree
diff --git a/scpipelines/pipeline_quantcells.py b/scpipelines/pipeline_quantcells.py
@@ -199,7 +199,9 @@ def run_kallisto_bus(infiles, outfile):
 
     job_memory = PARAMS['bustools_memory']
 
-    P.run(statement, job_options='-t 167:00:00')
+
+     P.run(statement, job_options='-t 24:00:00')
+
 
 
 @jobs_limit(1)
@@ -268,7 +270,7 @@ def bustools_count(infile, outfile):
 
 
     statement = """bustools count -o %(out_dir)s -g %(tr2g)s -e %(mat)s -t %(trans)s --genecounts 2> %(out_dir)s.count.log %(infile)s"""
-    P.run(statement)
+    P.run(statement, job_options='-t 24:00:00')
 
 
 @active_if(PARAMS['mixed_species'])

diff --git a/scpipelines/seurat/pipeline_qc-1/Rmarkdown/QC.Rmd b/scpipelines/seurat/pipeline_qc-1/Rmarkdown/QC.Rmd
@@ -191,7 +191,7 @@ for(i in 1:length(so)){
     
     # run emptydrops
     set.seed(1)
-    out <- DropletUtils::emptyDrops(assay(sce[[i]], "counts"), lower = 100)
+    out <- DropletUtils::emptyDrops(assay(sce[[i]], "counts"), lower = ini$UMI_filter)
     
     # add emptydrops info to colData
     sce[[i]]@colData$empty_drops_FDR <- out$FDR

diff --git a/scpipelines/seurat/pipeline_qc-1/pipeline.yml b/scpipelines/seurat/pipeline_qc-1/pipeline.yml
@@ -17,7 +17,7 @@ mirror: useast
 so_filter: 100
 
 #Specificy the number of counts if more stringent filter is required
-UMI_filter: 100
+UMI_filter: 300
 
 #Specify the format of output files
 output: seurat_object