WES -> capseq, WES is a specific type of capture sequencing.

ilus/main.py

@@ -14,7 +14,7 @@
 
 # Import specific functions of ilus
 from ilus.pipeline import (
-    create_wgs_pipeline_command, create_wes_pipeline_command, WGS,
+    create_wgs_pipeline_command, create_capseq_pipeline_command, WGS,
     create_genotype_joint_calling_command, genotypeGVCFs,
     create_vqsr_command, variantrecalibrator
 )
@@ -93,7 +93,7 @@ def parse_commandline_args():
     create_wgs_pipeline_command(commands)
 
     # The arguments for the whole pipeline of WES.
-    create_wes_pipeline_command(commands)
+    create_capseq_pipeline_command(commands)
 
     # The arguments for joint-calling process
     create_genotype_joint_calling_command(commands)
@@ -131,8 +131,8 @@ def run_command(args):
         aione = {"config": load_config(args.sysconf)}
         WGS(args, aione)
 
-    # Create WES pipeline. WES could re-use the same processes of WGS.
-    elif args.command == "WES":
+    elif args.command == "capseq":
+        # Create pipeline for capture-sequencing. WES is one kind of capture sequencing.
         aione = {"config": load_config(args.sysconf)}
         WGS(args, aione, is_capture_seq=True)
 

ilus/pipeline/__init__.py

@@ -1,6 +1,6 @@
 from ._command_args import (
     create_wgs_pipeline_command,
-    create_wes_pipeline_command,
+    create_capseq_pipeline_command,
     create_genotype_joint_calling_command,
     create_vqsr_command
 )

ilus/pipeline/_command_args.py

@@ -145,25 +145,27 @@ def create_wgs_pipeline_command(commands):
     return wgs_cmd
 
 
-def create_wes_pipeline_command(commands):
+def create_capseq_pipeline_command(commands):
     """All the arguments for creating WES pipeline."""
     # Todo: 思考要不要把这个参数改为 capseq，意思就是这个功能泛化为捕获测序数据分析流程，WES 只是捕获测序的一个特例？
-    wes_cmd = _add_germline_short_variant_discovery_argument(
+    capseq_cmd = _add_germline_short_variant_discovery_argument(
         commands.add_parser(
-            "WES",
+            "capseq",
             parents=[_parent_parser()],
-            help="Create pipeline scripts for WES (from FASTQ to genotype VCF).")
+            help="Create pipeline scripts for capture sequencing data (from FASTQ to genotype VCF). "
+                 "Whole-exome sequencing (WES) belong to capture sequencing, which only captures "
+                 "the coding regions of the genome.")
     )
 
-    wes_cmd.add_argument(
+    capseq_cmd.add_argument(
         "--capture-interval",
         dest="interval",  # WES capture region file (BED/Picard,1-based)
         type=str,
         required=True,
-        help="WES capture intervals: string or file (BED/Picard)"
+        help="Capture intervals, must be a file path: (BED/Picard) file"
     )
 
-    return wes_cmd
+    return capseq_cmd
 
 
 def create_genotype_joint_calling_command(commands):

ilus/pipeline/_germline_short_variant_discovery.py

@@ -160,7 +160,8 @@ def _fetch_calling_variants_interval(kwargs, aione: dict = None, is_capture_seq:
         if is_capture_seq:
             # 如果是 capture sequence 比如 WES，把该文件记录起来，该 key 只为种情况而添加。
             if (type(kwargs.interval) is not str) or (not Path(kwargs.interval).is_file()):
-                sys.stderr.write(f"[Error] --capture-interval must be a file, but got {kwargs.interval}\n")
+                sys.stderr.write(f"[Error] --capture-interval must be a file, "
+                                 f"but got {kwargs.interval}\n")
                 sys.exit(1)
 
             aione["config"]["capture_interval_file"] = kwargs.interval

tests/README.md

@@ -46,5 +46,5 @@ ilus WGS -c -n my_wgs -C ilus_sys.yaml -I sample_fastq.list -O ./tmp --use-senti
 ilus WGS -c -n my_wgs -C ilus_sys.yaml -I sample_fastq.list -O ./tmp -f --interval human_GRCh38.calling_interval.bed
 
 ## WES
-ilus WES -c -n my_wgs -C ilus_sys.yaml -I sample_fastq.list --capture-interval human_GRCh38.calling_interval.bed -O ./tmp -f
-ilus WES -c -n my_wgs -C ilus_sys.yaml -I sample_fastq.list --capture-interval human_GRCh38.calling_interval.bed -O ./tmp -f --use-sentieon
+ilus capseq -c -n my_wgs -C ilus_sys.yaml -I sample_fastq.list --capture-interval wes.test_interval.bed -O ./tmp -f
+ilus capseq -c -n my_wgs -C ilus_sys.yaml -I sample_fastq.list --capture-interval wes.test_interval.bed -O ./tmp -f --use-sentieon