Category: Uncategorized

Hands On

The figure below depicts the simple pipeline we will build. Note the dependencies (indicated with arrows) and the steps which run in parallel (same row). Launch interactive session
srun -c2 -t1:00:00 --mem=10000 --pty /bin/bash

Load nextflow
module load nextflow/20.01.0

Make the config file
params.reads = "/scratch/mk5636/nextflow-badas/data/*.fastq.gz"
params.ref = "/scratch/work/cgsb/genomes/Public/Fungi/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa"
params.out = "$SCRATCH/nextflow-badas/out"
workDir = params.out + '/nextflow_work_dir'

Building the workflow (main.nf)

// Setup the reference file
 ref = file(params.ref)

// Custom filenames
Channel
     .fromFilePairs( params.reads, size: -1)
     { file -> file.getBaseName() - ~/_n0[12]/ - ~/.fastq/ }
     .ifEmpty { error "No reads matching: ${params.reads}"  }
     .set { read_pairs_ch }

// Standard Illumina filenames
//Channel
//     .fromFilePairs( params.reads )
//     .ifEmpty { error "No reads matching: ${params.reads}"  }
//     .set { read_pairs_ch }

process align {
    publishDir "${params.out}/aligned_reads", mode:'copy'

    input:
    set pair_id, file(reads) from read_pairs_ch

    output:
    set val(pair_id), file("${pair_id}_aligned_reads.sam") into aligned_reads_ch

    script:
    """
    module load bwa/intel/0.7.17
    bwa mem \
        $ref \
        ${reads[0]} \
        ${reads[1]} \
        > ${pair_id}_aligned_reads.sam
    """
}

process sort_index_reads {
}

process aligned_read_stats {
}

Using Slurm (add this to your config file)

process {
    executor = 'slurm'
    cpus = 10
    memory = '30 GB'
    time = '30 min'
    withName: align_reads { cpus = '20'}
}

Using sbatch to submit your workflow

 #!/bin/bash 

 #SBATCH –nodes=1
 #SBATCH –ntasks-per-node=1
 #SBATCH –cpus-per-task=2
 #SBATCH –time=5:00:00
 #SBATCH –mem=2GB
 #SBATCH –job-name=myJob
 #SBATCH –output=slurm_%j.out

 module purge
 module load jdk/1.8.0_111
 module load nextflow/20.01.0

 nextflow run main.nf -c your.config