call Jasen, Rscript and ReporTree

#!/usr/bin/env bash

# Run Jasen
nextflow run /home/halfdan/projects_u_22_04/jasen/main.nf \
-profile staphylococcus_aureus 
-config /home/halfdan/projects_u_22_04/jasen/configs/nextflow.base.config \
--csv /mnt/arkiv02/8_Bioinformatics/Halfdan_arkiv02/wsl_ubuntu/run_jasen/sample_lists/sample_list4.csv

# Run r-script to extract cgMLST profile from Jasen output, translate missing data codes to zeros and create fake metadata file
# Rscript -e 'install.packages("rjson","tidyverse")
Rscript extract_cgmlist_from_json.R /mnt/arkiv02/8_Bioinformatics/Halfdan_arkiv02/wsl_ubuntu/run_jasen/out/saureus/analysis_result/ ./outputs/cg_mlst_1.xlsx 

# Run reportree

python reportree.py -m ./input/metadata.tsv \
-a ./input/cg_mlst_1.txt --columns_summary_report country,n_country,source \
-out ./output_examples/kvalitets_utskick_utbrottsutr_MRSA/grapetree_MSTreeV2/clust_thres_0/kvalitets_utskick_utbrottsutr_MRSA \
--analysis grapetree \
--method MSTreeV2 -thr 0