This is documentation for cg commands.
Recurring nomenclature:
- sample_id = internal sampleID, provided by LIMS:
ADM.. - ext_sample_id = external sampleID, provided by customer:
customer's sample_id - customer_id =
custxxx - ticket_id =
898988 - family_id =
cuddlygull
Add new things to statusDB.
Add a new customer with a unique INTERNAL_ID and NAME.
$ cg add customer CUSTOMER_ID CUSTOMER_NAME
where CUSTOMER_ID our internal customer ID, e.g. cust000, and CUSTOMER_NAME is the customer name, e.g. institute or P.I.
Add a family to CUSTOMER_ID with a NAME.
$ cg add family CUSTOMER_ID FAMILY_NAME
where FAMILY_NAME is the customer's familyID.
It is required to supply a panel.
$ cg add family --panel PANEL CUSTOMER_ID FAMILY_NAME
where PANEL are the gene panels. To add multiple panels simply provide --panel PANEL again with another gene panel.
When adding a family, set the priority by using
$ cg add family --priority PRIORITY CUSTOMER_ID FAMILY_NAME
where PRIORITY could be low, normal, or high.
Create a link between a FAMILY_ID and a SAMPLE_ID.
$ cg add relationship FAMILY_ID SAMPLE_ID
where FAMILY_ID is our internal family ID, e.g. cuddlygull.
It is required to set the status.
cg add relationship --status STATUS FAMILY_ID SAMPLE_ID
where STATUS can be affected, unaffected, or unknown.
Add relationship between parents using the --mother and --father flags. Example:
$ cg add relationship --mother MOTHER_ID FAMILY_ID SAMPLE_ID
where MOTHER_ID is the sampleID for the mother of the child sample.
Add a sample for CUSTOMER_ID with a SAMPLE_NAME.
$ cg add sample CUSTOMER_ID SAMPLE_NAME
where SAMPLE_NAME is the customer's sampleID.
It is required to set the gender of the sample.
$ cg add sample --sex SEX CUSTOMER_ID SAMPLE_NAME
where SEXcan be male, female, or unknown.
It is also required to set the application tag.
$ cg add sample --application APP_TAG CUSTOMER_ID SAMPLE_NAME
where APP_TAG is the application tag.
Add a LIMS id by using the ´--lims´ flag.
$ cg add sample --lims LIMS_ID CUSTOMER_ID SAMPLE_NAME
Add the order the sample belongs to by using the --order flag.
$ cg add sample --order TICKET_ID CUSTOMER_ID SAMPLE_NAME
Add the priority of the sample by using the --priority flag.
$ cg add sample --priority PRIORITY CUSTOMER_ID SAMPLE_NAME
where PRIORITY can be research, standard, priority, or express.
In case that the sample has been downsampled, provide how many reads it has been downsampled to.
$ cg add sample --downsampled INTEGER CUSTOMER_ID SAMPLE_NAME
Add a new user with an EMAIL (login) and a NAME (full). $ cg add user EMAIL NAME
It is required to connect the user to a customer. $ cg add user --customer CUSTOMER_ID EMAIL NAME
To give a user admin rights, use the --admin flag. $ cg add user --admin EMAIL NAME
Prepare and start a MIP analysis for a case. To do this use
$ cg analysis --family FAMILY_ID
where FAMILY_ID is the case name, e.g. cuddlygull.
Using this option will overwrite any configuration files, so if changes has been made to these that should be kept, use instead cg analysis start.
To change the quality of service for an analysis use
$ cg analysis --family FAMILY_ID --priority PRIORITY
where PRIORITY could be low, normal, or high. The default is set in statusDB.
Notification of errors will by default be sent to the email of the user who started the analysis. To change the email use
$ cg analysis --family FAMILY_ID --email TEXT
where TEXT is the email address.
Start all analyses that are ready for analysis.
Generate a configuration file (pedigree.yaml) for an analysis.
$ cg analysis config FAMILY_ID
To print the config to console, rather then creating the pedigree.yaml, use the --dry flag:
$ cg analysis config --dry FAMILY_ID
Link FASTQ files for a sample.
$ cg analysis SAMPLE_ID
To link files for an entire case, use the --family flag:
$ cg analysis link --family FAMILY_ID
Write aggregated gene panel file.
$ cg analysis panel FAMILY_ID
To only print the panel to console, rather than saving it to a file, use the --print flag:
$ cg analysis panel --print FAMILY_ID
Start the analysis pipeline for a family.
$ cg analysis start FAMILY_ID
To change the quality of servive for an analysis use
$ cg analysis start --priority PRIORITY FAMILY_ID
where PRIORITY could be low, normal, or high. The default is set in statusDB.
Backup utilities.
Fetch the first flowcell in the requested queue from backup.
$ cg backup fetch-flowcell --flowcell FLOWCELL_ID
Remove stuff. Use caution.
Remove analysis output. Removes the family directory (as defined in the cg config).
$ cg clean mip SAMPLE_INFO
where SAMPLE_INFO is the path to the familyID_qc_sample_info.yaml file
There is an option to skip confirmation: --yes
Automatically clean up "old" analyses. Removes all the family directories before the date defined by the user.
$ cg clean mipauto BEFORE_STR
where BEFORE_STR is a date in string format, e.g. 2018-04-19
There is an option to skip confirmation: --yes
Cleans the bam and bai files of selected bundle in housekeeper.
$ cg clean scout BUNDLE
There is an option to skip confirmation: --yes
Automatically clean up solved and archived scout cases. Cleans the bam and bai files in housekeeper.
cg clean scoutauto
Deliver stuff.
Link files from HK to customer inbox.
$ cg deliver inbox FAMILY_ID
where FAMILY_ID is the case name, e.g. cuddlygull.
--dry flag has not been implemented yet.
To just deliver a specific analysis version, use the --version flag, example:
$ cg deliver inbox --version 2018-04-19 FAMILY_ID
To only link specific types of files from HK, tags can be employed:
$ cg deliver inbox --tag TAG FAMILY_ID where TAG are the housekeeper tag(s)
If you want to deliver to another customer inbox than stated in statusDB, use
$ cg deliver inbox --inbox CUSTOMER_ID FAMILY_ID
where CUSTOMER_ID is the customerID.
Get information about records in the database.
The option -i makes a guess what type you are looking for.
$ cg get -i TEXT
where TEXT is a familyID, flowcellID, or sampleID.
Get information about a family.
$ cg get family FAMILY_ID
where FAMILY_ID is the familyID, e.g. cuddlygull.
The same information can be reached using options --customer and --name, instead of the familyID. Example:
$ cg get family --name FAMILY_NAME --customer CUSTOMER_ID
where FAMILY_NAME is the customer's internal familyID.
It is possible to toggle if related samples should be shown or not, using --samples or --no-samples. Example:
$ cg get family --no-samples FAMILY_ID
By default the related samples are shown.
Get information about a flowcell and the samples on it.
$ cg get flowcell FLOWCELL_ID
It is possible to toggle if related samples should be shown or not , using --samples or --no-samples. Example:
$ cg get flowcell --no-samples FLOWCELL_ID
By default the related samples are shown.
Get information about a sample.
$ cg get sample SAMPLE_ID
It is possible to toggle if related families should be shown or not , using --families or --no-families. Example:
$ cg get sample --no-families SAMPLE_ID
By default the related families are shown.
It is also possible to display related flowcells with the --flowcells option.
$ cg get sample --flowcells SAMPLE_ID
Do not touch this, please.
Setup the database.
$ cg init
Options for resetting database before setting up tables (--reset) and for bypassing manual confirmation (--force).
Update information in statusDB.
Update information about a family.
$ cg set family FAMILY_ID
where FAMILY_ID is the case name, e.g. cuddlygull.
To update the analysis action for the family, use
$ cg set family --action ACTION FAMILY_ID
where ACTION can be analyze, running, or hold.
To update the priority of the analysis, use
$ cg set family --priority PRIORITY FAMILY_ID
where PRIORITY can be research, standard, priority, or express.
To update the gene panel for an analysis, use
$ cg set family --panel PANEL FAMILY_ID
where PANEL are the gene panels. To add multiple panels simply provide --panel PANEL again with another gene panel.
Update information about a sample.
$ cg set sample SAMPLE_ID
To update the gender of a sample, use
$ cg set sample --sex SEX
where SEXcan be male, female, or unknown.
Update the customer, input format custXXX with XXX the customer number.
-c, --customer CUSTOMER_ID
To append a note/comment to a sample, put text between quotation marks! This will not overwrite the current comment.
-n, --note TEXT
Set number of downsampled total reads. Enter 0 to reset.
-d, --downsampled-to INTEGER
Set the application tag. Validation of the tag will be performed.
-a, --application-tag APPLICATION_TAG
Set the capture kit. NO validation of the kit will be performed.
-k, --capture-kit CAPTURE_KIT
View status of things.
Shows which families will be analyzed.
$ cg status analysis
View status of families.
$ cg status families
There is an option to skip initial records:
$ cg status families --skip INTEGER
where INTEGER is the number of lines that should be skipped (shows by default the 30 first entries).
View status of samples.
$ cg status samples --skip INTEGER
where INTEGER is the number of lines that should be skipped (shows by default the 30 first entries).
Store results from MIP in housekeeper.
Store a finished analysis in Housekeeper.
$ cg store analysis CONFIG_STREAM
where CONFIG_STREAM is the path to the configuration file.
Store all completed analyses.
$ cg store completed
Transfer results to the status interface.
Populate results from a flowcell.
$ cg transfer flowcell FLOWCELL_ID
Check if samples have been updated in LIMS.
$ cg transfer lims --status STATUS
where STATUS can be received, prepared, or delivered.
Upload results from analyses.
To upload analysis results to all the apps, use the flag --family. Example:
$ cg upload --family FAMILY_ID
where FAMILY_ID is our internal familyID, e.g. cuddlygull.
Upload all completed analyses to all the apps.
$ cg upload auto
Upload coverage from an analysis to Chanjo.
$ cg upload coverage FAMILY_ID
To re-upload an already existing analysis, use:
$ cg upload coverage --re-upload FAMILY_ID
Upload genotypes from an analysis to Genotype.
$ cg upload genotypes FAMILY_ID
Upload observations from an analysis to LoqusDB.
$ cg upload observations FAMILY_ID
Upload variants from analysis to Scout.
$ cg upload scout FAMILY_ID
To re-upload already existing analysis to scout, use:
$ cg upload scout --re-upload FAMILY_ID
It is possible to get the config values printed to the console:
$ cg upload scout --print FAMILY_ID
Validate a family of samples.
$ cg upload validate FAMILY_ID