put 10X config parameter into separate file

scripts/cellranger_config.py

@@ -0,0 +1,78 @@
+# work folder
+STATS_AREA = "/igo/stats/CELLRANGER/"
+
+# config info 
+ACCESS = 0o775
+config_dict = {
+    "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-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 "
+        }
+    },
+    "atac_count": {
+        "tool": " /igo/work/nabors/tools/cellranger-atac-2.1.0/cellranger-atac count ",
+        "genome": {
+            "Human": " --reference=/igo/work/nabors/genomes/10X_Genomics/ATAC/refdata-cellranger-atac-GRCh38-1.0.1 ",
+            "Mouse": " --reference=/igo/work/nabors/genomes/10X_Genomics/ATAC/refdata-cellranger-atac-mm10-1.1.0 "
+        }
+    },
+    "cnv": {
+        "tool": " /igo/work/nabors/tools/cellranger-dna-1.1.0/cellranger-dna cnv ",
+        "genome": {
+            "Human": " --reference=/igo/work/nabors/10X_Genomics/CNV/refdata-GRCh38-1.0.0 ",
+            "Mouse": " --reference=/igo/work/nabors/10X_Genomics/CNV/refdata-GRCm38-1.0.0 "
+        }
+    },
+    "multi": {
+        "tool": " /igo/work/nabors/tools/cellranger-8.0.0/cellranger multi "
+    },
+    "arc": {
+        "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-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 "
+        },
+        "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-3.0.0/external/tenx_feature_references/targeted_panels/Visium_Mouse_Transcriptome_Probe_Set_v1.0_mm10-2020-A.csv",
+            "Mouse_HD": "/igo/work/nabors/tools/spaceranger-3.0.0/external/tenx_feature_references/targeted_panels/Visium_Mouse_Transcriptome_Probe_Set_v2.0_mm10-2020-A.csv"
+        }
+    }
+}
+
+# cellranger command line options
+OPTIONS = " --nopreflight --jobmode=lsf --mempercore=64 --disable-ui --maxjobs=200"
+
+# 10X recipe list for different pipelines
+COUNT_FLAVORS = ["10X_Genomics_GeneExpression-3", "10X_Genomics_GeneExpression-5"]
+VDJ_FLAVORS = ["10X_Genomics_VDJ"]
+ATAC_FLAVORS = ["10X_Genomics_ATAC"]
+CNV_FLAVORS = ["10X_Genomics_CNV"]
+ARC_FLAVORS = ["10X_Genomics_Multiome", "10X_Genomics_Multiome_ATAC", "10X_Genomics_Multiome_GeneExpression"]
+SPATIAL_FLAVORS = ["10X_Genomics_Visium"]
+
+# we do not want to PROCESS SAIL (15500) or SCRI (12437) projects
+SCRI = "12437"
+SAIL = "15500"
+DO_NOT_PROCESS = [SCRI, SAIL]
+
+VISIUM_ENDPOINT = "https://igolims.mskcc.org:8443/LimsRest/getConfig?igoId="
+original_tiff_images_directory = "/rtssdc/mohibullahlab/IGO_Pipeline_Results/Single_Cell/10X_Genomics/TIFF_Images/"
+tiff_images_directory = "/igo/work/igo/TIFF_Images/"

scripts/cellranger_spatial.py

@@ -1,17 +1,10 @@
 import pandas as pd
-import sys
 import os
 import json
 import os.path
 import requests
 import shutil
-import glob
-
-
-ENDPOINT = "https://igolims.mskcc.org:8443/LimsRest/getConfig?igoId="
-original_tiff_images_directory = "/rtssdc/mohibullahlab/IGO_Pipeline_Results/Single_Cell/10X_Genomics/TIFF_Images/"
-tiff_images_directory = "/igo/work/igo/TIFF_Images/"
-
+import scripts.cellranger_config as CONFIG
 
 # sample_id can be get from sample sheet, will be the part in front of _IGO_
 class Spatial_sample:
@@ -28,7 +21,7 @@ def __init__(self, sample, project_id):
         self.copy_json(project_id)
 
     def get_info_from_LIMS(self):
-        response = requests.get(ENDPOINT + self.IGO_ID , auth = ("pms", "tiagostarbuckslightbike"), verify = False)
+        response = requests.get(CONFIG.VISIUM_ENDPOINT + self.IGO_ID , auth = ("pms", "tiagostarbuckslightbike"), verify = False)
         response_data = json.loads(response.text.encode("utf8"))
         self.chip_position = response_data["chipPosition"]
         self.chip_id = response_data["chipID"]
@@ -37,8 +30,8 @@ def get_info_from_LIMS(self):
 
     def copy_tiff(self, project_id):
         # project_id format as Project_12345
-        source_loc_dir = original_tiff_images_directory + project_id
-        destination_loc = tiff_images_directory + project_id
+        source_loc_dir = CONFIG.original_tiff_images_directory + project_id
+        destination_loc = CONFIG.tiff_images_directory + project_id
         destination_file = destination_loc + "/" + self.sample_name + ".tif"
         # create TIFF_images director if not exists
         if not os.path.exists(destination_loc):
@@ -56,8 +49,8 @@ def copy_tiff(self, project_id):
     # copy json file if exists
     def copy_json(self, project_id):
         # project_id format as Project_12345
-        source_loc = original_tiff_images_directory + project_id + "/json/" + self.sample_name + ".json"
-        destination_loc = tiff_images_directory + project_id
+        source_loc = CONFIG.original_tiff_images_directory + project_id + "/json/" + self.sample_name + ".json"
+        destination_loc = CONFIG.tiff_images_directory + project_id
         destination_file = destination_loc + "/" + self.sample_name + ".json"
 
         # create director if not exists