getting ready for version 2

Author: Edwin

manifest

@@ -1,14 +1,15 @@
-# Seurat.Preprocessing  urn:lsid:genepattern.org:module.analysis:00415:0.22
-#Tue Nov 17 02:06:02 UTC 2020
+# Seurat.Preprocessing  urn:lsid:genepattern.org:module.analysis:00415:2
+#Wed Jul 14 02:04:26 UTC 2021
 JVMLevel=
-LSID=urn\:lsid\:genepattern.org\:module.analysis\:00415\:0.22
-author=Edwin F. Juarez;UCSD - Mesirov Lab
-categories=preprocess & utilities;preprocess & utilities;single-cell;single-cell
+LSID=urn\:lsid\:genepattern.org\:module.analysis\:00415\:2
+author=Edwin F. Juarez & Jonathan Zamora;UCSD - Mesirov Lab
+categories=preprocess & utilities;single-cell
 commandLine=Rscript --no-save --quiet --no-restore <libdir>seurat_preprocess.R --input_rds <input_rds> --min_n_features <min_n_features> --max_n_features <max_n_features> --max_percent_mitochondrial <max_percent_mitochondrial> --norm_method <norm_method> --scale_factor <scale_factor> --feat_sel_method <feat_sel_method> --num_features <num_features> --num_to_label <num_to_label> --vdl_num_dims <vdl_num_dims> --vdhm_num_dims <vdhm_num_dims> --cells <cells> --file_name <file_name>
 cpuType=any
 description=Seurat preprocessing
+documentationUrl=https\://github.com/genepattern/Seurat.Preprocessing/blob/develop/doc.md
 fileFormat=rds
-job.docker.image=genepattern/seurat-suite\:2.4
+job.docker.image=genepattern/seurat-suite\:4.0.3
 language=any
 name=Seurat.Preprocessing
 os=any
@@ -182,8 +183,10 @@ p9_prefix_when_specified=
 p9_type=java.lang.Integer
 p9_value=
 privacy=public
+publicationDate=11/20/2020 01\:10 
 quality=development
+src.repo=https\://github.com/genepattern/Seurat.Preprocessing
 taskDoc=doc.html
 taskType=preprocess & utilities
 userid=edjuaro
-version=Editing parameter groups
+version=Upgrading to Seurat v4.0.3

run_seurat.sh

@@ -1,11 +1,11 @@
-docker run -v $PWD:/LOCAL -w $PWD/Job_1 -t genepattern/seurat-suite:2.4 Rscript --no-save --quiet --slave --no-restore  /LOCAL/seurat_preprocess.R\
- --tenx_data_dir 'https://s3-us-west-2.amazonaws.com/10x.files/samples/cell/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz' \
+docker run -v $PWD:/LOCAL -w $PWD/Job_1 -t genepattern/seurat-suite:4.0.3 Rscript --no-save --quiet --slave --no-restore  /LOCAL/src/seurat_preprocess.R\
+ --input_rds '/LOCAL/data/test_run.rds' \
  --column_name "percent.mt" --pattern 'MT-'\
  --first_feature 'nFeature_RNA' --second_feature 'nCount_RNA' --third_feature 'percent.mt'\
- --min_n_features 200 --max_n_features 2500 --max_percent_mitochondrial 5\
+ --min_n_features 2 --max_n_features 6000 --max_percent_mitochondrial 25\
  --norm_method 'LogNormalize' --scale_factor 10000\
  --num_features 2000 --num_to_label 10\
  --vdl_num_dims 2\
  --vdhm_num_dims 15 --cells 500\
  --file_name "test_run"\
- --keep_scale_data TRUE
+ --keep_scale_data TRUE