#!/bin/bash

genomes_dir=$1
fqPart_path="/home/mhussien/astrangia/zoe_2023/2023-decontamination/build/fqPart"
files=(
Ast25B
Ast26B
Ast27B
Ast28B
Ast29B
Ast30A
Ast34D
Ast35D
Ast36C
Ast42B
Ast44B
Ast45B
AW2C
AW3D
AW8D
)

parallel -j 5 $fqPart_path --R1 /home/mhussien/astrangia/zoe_2023/partitioning/raw_samples/{}_R1_001.fastq.gz --R2 /home/mhussien/astrangia/zoe_2023/partitioning/raw_samples/{}_R2_001.fastq.gz --genomes_dir $genomes_dir --kSize 21 --threads 5 ::: "${files[@]}"