sanibel_pb_docker.sh

#!/usr/bin/bash
#SBATCH --account=bphl-umbrella
#SBATCH --qos=bphl-umbrella
#SBATCH --job-name=sanibel
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=5
#SBATCH --mem=500gb
#SBATCH --time=48:00:00
#SBATCH --output=sanibel.%j.out
#SBATCH --error=sanibel.%j.err
#SBATCH --mail-user=<EMAIL>
#SBATCH --mail-type=FAIL,END

module load nextflow
APPTAINER_CACHEDIR=./
export APPTAINER_CACHEDIR

singularity exec docker://staphb/mlst:2.23.0 cp /mlst-2.23.0/db/pubmlst/neisseria/neisseria.txt ./
singularity exec  docker://staphb/mlst:2.23.0 cp /mlst-2.23.0/db/pubmlst/hinfluenzae/hinfluenzae.txt ./
nextflow run flaq_amr_plus2.nf -params-file params.yaml -c ./configs/docker.config
sort ./output/*/report.txt | uniq > ./output/sum_report.txt
sed -i '/sampleID\tspeciesID/d' ./output/sum_report.txt
sed -i '1i sampleID\tspeciesID_mash\tnearest_neighb_mash\tmash_distance\tspeciesID_kraken\tkraken_percent\tmlst_scheme\tmlst_st\tmlst_cc\tpmga_species\tserotype\tnum_clean_reads\tavg_readlength\tavg_read_qual\test_coverage\tnum_contigs\tlongest_contig\tN50\tL50\ttotal_length\tgc_content\tannotated_cds' ./output/sum_report.txt
rm ./neisseria.txt
rm ./hinfluenzae.txt

mv ./*.out ./output
mv ./*err ./output

dt=$(date "+%Y%m%d%H%M%S")
mv ./output ./output-$dt
#mv ./work ./work-$dt

rm -r ./work
rm -r ./cache