[IGBF-2945] Run trimmomatic on HPC system using nextflow and Singularity - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
None

Story Points:
1.5
Epic Link:
Deploy and maintain infrastructure
Sprint:
Fall 3 2021 Sep 13 - Sep 24

Description

To make our HPC data processing easier and more robust, we are exploring using the nextflow workflow management system in conjunction with Singularity containers.

For this task, develop a nextflow script that runs "trimmomatic" on all fastq files in a directory.

Attachments

Issue Links

relates to

IGBF-2909 Determine if and how we can use Nextflow on UNCC HPC cluster

Closed

Activity

Ascending order - Click to sort in descending order

Ann Loraine created issue - 15/Sep/21 5:16 PM

Ann Loraine made changes - 15/Sep/21 5:16 PM

Field	Original Value	New Value
Epic Link		IGBF-2323 [ 18477 ]

Ann Loraine made changes - 15/Sep/21 5:16 PM

Link

This issue relates to ~~IGBF-2909~~ [ ~~IGBF-2909~~ ]

Ann Loraine made changes - 15/Sep/21 5:16 PM

Rank

Ranked higher

Ann Loraine made changes - 15/Sep/21 5:16 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Ann Loraine made changes - 16/Sep/21 7:28 AM

Comment

[ Retrieving trimmomatic singularity image:

{code}
singularity pull trimmomatic_v0.39.sif oras://registry.forgemia.inra.fr/gafl/singularity/trimmomatic/trimmomatic:latest
{code}

Worked fine on a head node, but failed due to a network error of some time when run from an Andromeda partition interactive session.
]

Ann Loraine made changes - 17/Sep/21 11:55 AM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Ann Loraine made changes - 17/Sep/21 3:36 PM

Comment

[ Final version of the nextflow script:

{code}
#!/usr/bin/env nextflow

// test on one sample: nextflow run trim2.nf --dev -with-singularity trimmomatic_v0.39.sif
// run all: runextflow run trim2.nf --dev -with-singularity trimmomatic_v0.39.sif
params.dev = false
params.number_of_inputs = 1
params.saveMode = 'copy'
//params.filePattern = "/projects/tomato_genome/rnaseq/phase2-rnaseq-Sep2021/*_{R1,R2}_001.fastq.gz"
params.filePattern = "fastq/*_{R1,R2}_001.fastq.gz"
params.outdir = 'results'

Channel
    .fromFilePairs( params.filePattern )
    .ifEmpty { error "Cannot find any reads matching: ${params.filePattern}" }
    .take( params.dev ? params.number_of_inputs : -1 )
    .set { read_pairs_ch }


process trim {
    time '2h'

    publishDir "$params.outdir", pattern: '*.fq.gz', mode: 'copy'

    input:
    tuple val(prefix), file(reads) from read_pairs_ch

    output:
    file '*.fq.gz'

    script:
    fq_1_paired = prefix + '_R1.p.fq'
    fq_1_unpaired = prefix + '_R1.u.fq'
    fq_2_paired = prefix + '_R2.p.fq'
    fq_2_unpaired = prefix + '_R2.u.fq'
    """
    trimmomatic \
    PE -phred33 \
    ${reads[0]} \
    ${reads[1]} \
    $fq_1_paired \
    $fq_1_unpaired \
    $fq_2_paired \
    $fq_2_unpaired \
    ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50
    gzip $fq_1_paired
    gzip $fq_1_unpaired
    gzip $fq_2_paired
    gzip $fq_2_unpaired
    """
}
{code}

Outputs copied to a results directory. ]