feat: Cell Ranger 9.0.0

README.md

@@ -3,5 +3,3 @@ Cell Ranger is a set of analysis pipelines that perform sample demultiplexing, b
 Please note that this source code is made available only for informational purposes. 10x does not provide support for interpreting, modifying, building, or running this code.
 
 The officially supported release binaries are available at <https://www.10xgenomics.com/support/software/cell-ranger/downloads>. Documentation is available at <https://www.10xgenomics.com/support/software/cell-ranger>.
-
-Note: This source code is for Cell Ranger 8.0.1. The source code for the latest Cell Ranger 9.0.0 release will be posted here soon.

bin/rna/mkgtf_lib.py

@@ -61,7 +61,7 @@ def main():
     for attribute_str in attributes_str:
         parts = attribute_str.split(":")
         if len(parts) != 2:
-            sys.exit("Attribute option must have format <key;value>: %s" % attribute_str)
+            sys.exit(f"Attribute option must have format <key;value>: {attribute_str}")
         key, value = parts
         attributes[key].add(value)
 

bin/sc_rna/mkfastq

@@ -15,7 +15,6 @@ function implement_read_configuration {
         TENX_UMI_START_INDEX=16
         TENX_UMI_LENGTH=10
         TENX_SI_READ_TYPE=I1
-        WHITELIST_NAME="737K-august-2016,3M-february-2018"
     else
         # 10x barcode in index read, v1 chemistry
         TENX_BC_READ_TYPE=I1
@@ -24,9 +23,7 @@ function implement_read_configuration {
         TENX_UMI_START_INDEX=0
         TENX_UMI_LENGTH=10
         TENX_SI_READ_TYPE=I2
-        WHITELIST_NAME="737K-april-2014_rc"
     fi
-    TENX_BARCODE_WHITELIST=$(python -c 'from sys import argv;import cellranger.barcodes.utils as u;print(u.get_barcode_whitelist_paths(argv[1]))' "$WHITELIST_NAME")
 }
 
 # shellcheck source=../tenkit/_mkfastq

bin/tenkit/_mkfastq

@@ -434,10 +434,6 @@ fi
 ##############################
 # Check environment variables
 #
-if [ -z "$TENX_BARCODE_WHITELIST" ]; then
-    echo "TENX_BARCODE_WHITELIST environment variable must be set by enclosing script."
-    exit 1
-fi
 
 if [ -z "$TENX_BC_READ_TYPE" ]; then
     echo "TENX_BC_READ_TYPE environment variable must be set by enclosing script."
@@ -585,7 +581,6 @@ call MAKE_FASTQS_CS(
     specs                 = $specs,
     project               = $project,
     bases_mask            = $bcl2fastq_use_bases_mask,
-    barcode_whitelist     = "$TENX_BARCODE_WHITELIST",
     bcl2fastq1_args       = $bcl2fastq1_opts,
     bcl2fastq2_args       = $bcl2fastq2_opts,
     bc_read_type          = "$TENX_BC_READ_TYPE",

bin/tenkit/check_fastq_params_lib.py

@@ -30,7 +30,7 @@ def get_mro_params(fastq_paths, fastqprefixes):
         print(f"{fastq_mode}\t{ensure_str(sample_name)}")
         sys.exit(0)
     except ValueError as ex:
-        sys.stderr.write("%s\n" % str(ex))
+        sys.stderr.write(f"{ex!s}\n")
         sys.exit(1)
 
 

bin/tenkit/check_fastq_paths_lib.py

@@ -36,7 +36,7 @@ def get_bcl2fastq_output_folder(path):
     :raises: ValueError if the path/project path is illegal
     """
     if not os.path.exists(path):
-        raise ValueError("Invalid path: %s" % path)
+        raise ValueError(f"Invalid path: {path}")
 
     link = os.path.join(path, "outs", "fastq_path")
     # check path pointed to pipestance
@@ -74,7 +74,7 @@ def main():
     for path in fastq_paths:
         abs_path = os.path.abspath(os.path.expanduser(path))
         if not os.path.exists(abs_path):
-            sys.stderr.write("Invalid path to --fastqs: %s\n" % abs_path)
+            sys.stderr.write(f"Invalid path to --fastqs: {abs_path}\n")
 
         try:
             fastq_path = get_bcl2fastq_output_folder(abs_path)
@@ -97,21 +97,19 @@ def main():
                 raise ValueError(
                     "The --project argument must be specified if BCLs "
                     "were demultiplexed into multiple project folders. "
-                    "Options:\n%s" % projects_list
+                    f"Options:\n{projects_list}"
                 )
             # project length == 1
             elif len(projects) == 1:
                 output_paths.append(os.path.join(fastq_path, projects[0]))
 
         except ValueError as ex:
-            sys.stderr.write("%s\n" % str(ex))
+            sys.stderr.write(f"{ex!s}\n")
             return 1
 
     # if no paths selected because --project specified, say so
     if args.project and len(fastq_paths) > 0 and len(output_paths) == 0:
-        sys.stderr.write(
-            "Could not find any paths that matched --project value: %s\n" % args.project
-        )
+        sys.stderr.write(f"Could not find any paths that matched --project value: {args.project}\n")
         return 1
 
     # at this point all paths containing either paths to the bcl2fastq root folder

bin/tenkit/upload_lib.py

@@ -27,7 +27,7 @@
 def _parse_args(argv: list[str]) -> tuple[str, str]:
     """Parse command line."""
     usage_message = """Usage:
-        %s upload <your_email> <file>""" % (
+        {} upload <your_email> <file>""".format(
         os.getenv("TENX_PRODUCT", "")
     )
 
@@ -161,7 +161,7 @@ def read(self, csize: int) -> bytes:
                 ("%d%%" % pctg).rjust(4),  # percentage
                 (("=" * (pctg // 3)) + ">").ljust(34),  # progress bar
                 pn(self.bcount).rjust(len(pn(self.bsize))),  # bytes sent
-                ("%.2fMb/s" % mbps).rjust(10),  # bitrate
+                (f"{mbps:.2f}Mb/s").rjust(10),  # bitrate
                 ("%dm" % etam),  # eta min
                 ("%ds" % etas).rjust(3),  # eta sec
             )
@@ -202,7 +202,7 @@ def _upload(filename: str, size: int, upurl: str, context: ssl.SSLContext):
             print("\nError:")
             root = ET.fromstring(contents)
             for e in root:
-                if e.tag != "RequestId" and e.tag != "HostId":
+                if e.tag not in ("RequestId", "HostId"):
                     print(f"   {e.tag}: {e.text}")
         else:
             print("\nUpload complete!")