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The nf-core/bactmap workflow requires Nextflow to be installed in your account on the HPC. Find details on how to install and test Nextflow here prepare a nextflow.config file and run a PBS pro submission script for Nextflow pipelines.

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Usage: https://nf-co.re/bactmap/1.0.0/usage

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Interactive session on the HPC

qsub -I -S /bin/bash -l walltime=10:00:00 -l select=1:ncpus=2:mem=4gb

SRA TOOLKIT

Use singularity container to fetch public data on the HPC:

1. One file at a time:

singularity run docker://ncbi/sra-tools:latest prefetch SRR1198667

singularity run docker://ncbi/sra-tools:latest fastq-dump -X 1000000 -I --split-files SRR1198667

2. use a list:

singularity run docker://ncbi/sra-tools:latest prefetch --option-file SraAccList.txt

singularity run docker://ncbi/sra-tools:latest fastq-dump -X 1000000 -I --split-files SRR1198667

3.a compress the fastq files

gzip -c filename.fastq > filename.fastq.gz

3.b alternatively run a loop to compress all fastq files in the folder:

for file in `ls *.fastq`; do echo $file; gzip -c $file > ${file}.gz; done

Getting Started

Download and run the workflow using a minimal data provided by nf-core/bactmap. We recommend using singularity as the profile for QUT’s HPC. Note: the profile option ‘docker’ is not available on the HPC.

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Note: at this time, the test profile will fail to run

Running the test - create a 'launch.pbs' script:

#!/bin/bash -l
#PBS -N nf-bactmap
#PBS -l walltime=24:00:00
#PBS -l select=1:ncpus=1:mem=5gb
cd $PBS_O_WORKDIR
NXF_OPTS='-Xms1g -Xmx4g'

module load java

#run test for bactmap
nextflow run nf-core/bactmap -profile test,singularity

submit the job:

qsub launch.pbs

check the job:

qjobs

Running the pipeline using custom data

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When specifying the path to the data files, it is more portable to use absolute paths rather than relative paths.

check if ascii characters were added in your samplesheet.csv file:

cat -A samplesheet.csv 

Creating the samplesheet.csv file using Excel can add ascii characters, run the following command to remove them:

dos2unix samplesheet.csv

Preparing to run on the HPC

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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 recombination using gubbins
    --rapidnj \ #build a RapidNJ tree
    --fasttree \ #build a RapidNJ tree
    --iqtree \ #build an IQ-TREE tree
    --raxmlng #build a RAxML-NG tree

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