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#!/bin/bash -l
#PBS -N bactmap02
#PBS -l select=1:ncpus=2:mem=4gb
#PBS -l walltime=24:00:00

cd $PBS_O_WORKDIR
module load java
NXF_OPTS='-Xms1g -Xmx4g'

nextflow run nf-core/bactmap \
    --input samplesheet.csv \
    --reference chromosome.fasta \
    -profile singularity \
    --trim reads --trim \ #trim reads
    --remove_recombination \ #remove recombiinationrecombination using gubbins
    --rapidnj \ #build a RapidNJ tree
    --fasttree \ #build a RapidNJ tree
    --iqtree \ #build an IQ-TREE tree
    --raxmlng #build a RAxML-NG tree