Generates the input configuration file required to run the rna-seq pipeline.
- Requires Python
>3.6.9 - Install required packages by running
pip3 install -r scripts/requirements.txt
usage: make_json_rnaseq.py [-h] [-g GCP_PATH] [-o OUTPUT_PATH]
[-r OUTPUT_REPORT_NAME] [-u] [-a {rat,human}]
[-n NUM_CHUNKS] [-d DOCKER_REPO] [-p PROJECT]
This script is used to generate input json files from the fastq_raw dir on gcp
for running rna-seq pipeline on GCP
optional arguments:
-h, --help show this help message and exit
-g GCP_PATH, --gcp_path GCP_PATH
location of the submission batch directory in gcp that
contains the fastq_raw dir
-o OUTPUT_PATH, --output_path OUTPUT_PATH
output path, where you want the input jsons to be
written
-r OUTPUT_REPORT_NAME, --output_report_name OUTPUT_REPORT_NAME
name of the output report to be written
-u, --undetermined Adding this flag will process undetermined FastQ files
if they exist. These are fastq files with prefix
"Undetermined_". If this flag isn't passed, items with
prefix "Undetermined_" will be removed
-a {rat,human}, --organism {rat,human}
organism name, e.g. rat or human
-n NUM_CHUNKS, --num_chunks NUM_CHUNKS
number of chunks to split the input files, should
always be <= number of input files
-d DOCKER_REPO, --docker_repo DOCKER_REPO
Docker repository prefix containing the images used in
the workflow
-p PROJECT, --project PROJECT
Project name on the google cloud platform
Example
python3 make_json_rnaseq.py -g gs://motrpac/rna-seq/test \
-o `pwd`/input_json \
-r rna-seq-test \
-a rat \
-n 1 \
-d gcr.io/motrpac-portal/motrpac-rna-seq-pipeline