pipeline.sh.template

#!/bin/bash
# version 1
# 0/50 0 0 ? * * * pipeline.sh >/dev/null 2>&1

# OUTPUT DIR
CACHE_DIR=/mnt/c/data/cache
DOWNLOAD_DIR=/mnt/c/data/prod_mpx
#
ANALYSIS_DATE=$(date +'%Y-%m-%d') # 2022-11-22
INPUT_FASTA=/mnt/c/data/prod_mpx/${ANALYSIS_DATE}/output/seq.min.fasta
INPUT_META=/mnt/c/data/prod_mpx/${ANALYSIS_DATE}/output/meta.tsv

CPUS=8
source /home/note/miniconda3/etc/profile.d/conda.sh

conda activate mpxsonar-dev
# 1.
# TODO: need to adjust the script to handle the parameters or arguments
# Right now just assume, there is the .env file in the same directory.
python NCBI.downloader.py --date $ANALYSIS_DATE -o ${DOWNLOAD_DIR}/${ANALYSIS_DATE}

# 2.
# Load into database
#sonar import -r MT903344.1 --fasta $INPUT_FASTA --tsv $INPUT_META --cols sample=ID --cache $CACHE_DIR/cache_MT903 --threads $CPUS
#sonar import -r ON563414.3 --fasta $INPUT_FASTA --tsv $INPUT_META --cols sample=ID --cache $CACHE_DIR/cache_ON563 --threads $CPUS
# sonar import -r ON585033.1 --fasta $INPUT_FASTA --tsv $INPUT_META --cols sample=ID --cache $CACHE_DIR/cache_ON585 --threads $CPUS
#sonar import -r NC_063383.1 --fasta $INPUT_FASTA  --tsv $INPUT_META --cols sample=ID --cache $CACHE_DIR/cache_NC063 --threads $CPUS
# sonar import -r ON568298.1 --fasta $INPUT_FASTA  --tsv $INPUT_META --cols sample=ID --cache $CACHE_DIR/cache_ON568 --threads $CPUS