Function list

config

Record the user’s AK, SK, endpoint and region parameters, eliminating the need for the user to manually input parameters again when using the main functions

$ popgen vol-pipe config
Enter ACCESS KEY ID: 
Enter ACCESS KEY SECRET: 
Enter region:
Enter TOS endpoint:

current support region in Volcengine is: cn-beijing

current support TOS endpoint in Volcengine is: tos-cn-beijing.volces.com, if your client is using a server in Volcengine Beijing, the endpoint is tos-cn-beijing.ivolces.com

copy-joint-res-meta

copy joint result file from meta table

Argument name(s)	Optional	Default value	Summary
-i, --input-joint-res	false		input joint result meta
-b, --target-bucket-path	false		target bucket path to copy split gvcf, tos://bucket_name/path/
-c, --column-list	false		column names of files to be copied, separated by commas
-t, --threads	false	8	multi threads to copy TOS file

delete-file

delete file with submission ID

Argument name(s)	Optional	Default value	Summary
-w, --workspace	false		the workspace you created submission
-s, --submission-id	true		the submission ID to request
-l, --submission-list	true		the submission ID list to request

get-germline-meta

get vol get-data-model input from fastq TOS path

Argument name(s)	Optional	Default value	Summary
-b, --bucket-path	false		TOS path of fastq files, tos://bucket_name/path/to/file
-o, --output	false		output file name of get-data-model

get-joint-meta

get vol get-data-model input from variant calling result meta

Argument name(s)	Optional	Default value	Summary
-i, --input-calling-res	false		input variant calling result meta
-o, --output-prefix	false		output file name prefix to joint meta
-b, --target-bucket-path	false		target bucket path to copy split gvcf, tos://bucket_name/path/
-t, --threads	false	8	multi threads to copy TOS file

pop-variant-calling

multi sample variant calling and joint calling pipeline

Argument name(s)	Optional	Default value	Summary
-c, --config	false		input config file in json format
-o, --outdir	false		output dir path

quick-submit

quick submit workflow with meta data corresponding to the workflow

Argument name(s)	Optional	Default value	Summary
-c, --config	false		input config file in JSON format，param names must match WDL inputs JSON
-o, --outdir	false		output directory path
-m --meta-data	false		the meta data of the samples you want to submit,
-a --app_name	false		workflow name,which workflow you want to run
--if-mount	true	False	if mount TOS, if True the input data will not take up disk space and data input to the computing environment will be faster.