metagenomics-pipeline.sh

#PBS -l walltime=3:00:00,mem=12gb,nodes=1:ppn=6

module load kraken
module load krona
module load humann2
module load kneaddata

#JOB KneadData
#INPUTS demo.fastq
#INPUTS  Homo_sapiens_Bowtie2_v0.1
#OUTPUTS demo_kneaddata_$DATABASE_bowtie2_contam.fastq FASTQ file containing reads that were identified as contaminants from the database (named $DATABASE).
#OUTPUTS demo_kneaddata.fastq: This file includes reads that were not in the reference database.
#OUTPUTS demo_kneaddata.trimmed.fastq: This file has trimmed reads.
#OUTPUTS demo_kneaddata.log
kneaddata --input demo.fastq --reference-db Homo_sapiens_Bowtie2_v0.1 --output kneaddata_output

#JOB Kraken
#INPUTS kneaddata_output/demo_kneaddata.trimmed.fastq
#INPUTS minikraken
#OUTPUTS kraken.out.txt
kraken --threads 6 --preload --fastq-input --output kraken.out.txt --db minikraken kneaddata_output/demo_kneaddata.trimmed.fastq

#JOB krona 
#INPUT kraken.out.txt
#OUTPUT kraken.krona.html
ktImportTaxonomy -o kraken.krona.html -t 3 -s 4 kraken.out.txt

#JOB HUMAnN2
#INPUT kneaddata_output/demo_kneaddata.trimmed.fastq
#OUTPUTS humann2/genefamilies.tsv
#OUTPUTS humann2/pathabudance.tsv
#OUTPUTS humann2/pathcoverage.tsv
#OUTPUTS humann2/metphlan_bug_list.tsv
humann2 --threads 6 --input kneaddata_output/demo_kneaddata.trimmed.fastq --output humann2