kevbrick / mahgoub2020

Analytic pipeline for Mahgoub et al. 2020 (Zcwpw1)

Mahgoub et al. 2020 (zcwpw1) nextflow pipeline :

This nextflow pipeline is configured to work on a SLURM-based HPC with modules. It can be relatively easily configured to run on other systems (see nextflow documentation : https://www.nextflow.io/).

Requirements:

Tools / programs :

• bedtools 2.27.1
• deeptools 3.0.1
• macs 2.1.2
• meme 5.0.1
• minimap2 2.17
• nextflow 0.30.2
• picard 2.9.2
• R 3.5.2
• samtools 1.9
• sratoolkit 2.9.2
• ucsc 388

NOTE: These are the recommended (and tested) version of each tool, however newer / older versions will work in most cases. One exception is older versions of nextflow, which will not work.

Global variables required:

$SLURM_JOBID : Specifies the temporary subfolder to use (see Temp folder requirements below)

Temp folder requirements

The pipeline requires a high-level temporary folder called /lscratch. On a SLURM-based HPC, each job is assigned a global id ($SLURM_JOBID) and this is appended to the temp folder name for each process. This is currently hard-coded. Thus, there is a requirement for :

/lscratch folder for temporary files SLURM_JOBID global variable for each HPC job.

Pipeline execution

RUN ON SLURM CLUSTER

nextflow run -c accessoryFiles/nxfConfig/nextflow.config \
    Zcwpw1_CutNRunPipe.nf \
    --outdir output \
    --getData \
    --projectdir `pwd` \
    -with-report Zcwpw1Pipeline.nxfReport.html \
    -with-trace Zcwpw1Pipeline.nxfTrace.html \
    -with-timeline Zcwpw1Pipeline.nxfTimeline.html

RUN ON LOCAL MACHINE

nextflow run -c accessoryFiles/nxfConfig/nextflow.local.config \
    Zcwpw1_CutNRunPipe.nf \
    --outdir output \
    --getData \
    --projectdir `pwd` \
    -with-report Zcwpw1Pipeline.nxfReport.html \
    -with-trace Zcwpw1Pipeline.nxfTrace.html \
    -with-timeline Zcwpw1Pipeline.nxfTimeline.html