Quick and dirty manual

generate_delivery_list

generate_delivery_list - an application to print validated data in stdout and incorrect data in stderr

SYNOPSIS

[ENV VARIABLES] generate_delivery_list [stdout redirections] [stderr redirections]

Some ENV VARIABLES

Only optionals because set by default.

DATA_ROOT_PATH: Folder where the application will scan for FLAGS and DATA. Default: /mnt/ngsdata/WGS/

DRAGEN_VALIDATOR_DIR: dragen-validator installation dir. Used to find the generate_delivery_list.awk script. Default: folder of the generate_delivery_script

REGEX_FILE: file used to describe cases and corresponding messages. Default: "${DRAGEN_VALIDATOR_DIR}/assets/regex.tsv"

DEBUG: will keep temporary files in /tmp/ for debug and will print paths on stderr. Will also add DROPBOX_DATA_FOLDER in the output lists.

Some exemples

By correctly redirecting stdout and stderr, you can easily save or view the results.

1. Save stdout in delivery_list.tsv and ignore the stderr :

generate_delivery_list > delivery_list.tsv 2>/dev/null

2. Save stdout in delivery_list.tsv and stderr in error_list.tsv :

generate_delivery_list > delivery_list.tsv 2> error_list.tsv

generate_delivery_list > delivery_list.tsv 2>/dev/null

We can easly format

By using pspg, we can access to a TSV viewer, sort data and search. Start by loading the module with module load pspg/5.5.3. Details about the pspg commands here.

1. View only the delivery list :

generate_delivery_list 2>/dev/null | pspg --tsv

2. View only the list of errors :

generate_delivery_list 2>&1 >/dev/null | pspg --tsv

dragen-validator

dragen-validator - a fast pipeline to check, copy and flag DATA, following MY_ORG business rules.

Some ENV VARIABLES

DATA_ROOT_PATH: Folder where the application will scan for FLAGS and DATA. Default: /mnt/ngsdata/WGS/

RESULTS_ROOT_PATH: Folder where the application will save each instance of results. Default: TODO

Options

--delivery_list TSV_DELIVERY_LIST: TSV file generated from generate_reports stdout. MANDATORY

--dry [true|false]: perform a trial run with no changes made (default true)

-resume: resume the latest run of dragen-validator. Useful for recovering from errors.

Some exemples

dragen-validator --delivery_list delivery_list.tsv