Freebayes parallelization using nextflow
You will need a working version of nextflow, see here on how to install nextflow. Nextflow modules are avialable on some of the HPC computing resources.
See modules on HPC clusters
# === Nova
module load gcc/7.3.0-xegsmw4 nextflow
module load singularity
NEXTFLOW=nextflow
# === Condo
module load gcc/7.3.0-xegsmw4 nextflow
module load singularity
NEXTFLOW=nextflow
# === Ceres
module load nextflow
# singularity already available, no need for module
NEXTFLOW=nextflow
# === Atlas (will need a local install of nextflow and will need the --account "projectname" flag)
module load singularity
NEXTFLOW=/project/isu_gif_vrsc/programs/nextflow
nextflow run isugifNF/freebayes --help -r main
Usage:
The typical command for running the pipeline is as follows:
nextflow run main.nf --fastaReference genomeFile.fasta --bam /full/path/input/file.bam --vcf outputPrefix -profile singularity,nova
N E X T F L O W ~ version 20.07.1
Launching `isugifNF/freebayes` [stupefied_davinci] - revision: 0c1655da96 [draft_dsl2]
----------------------------------------------------
\\---------//
___ ___ _ ___ ___ \\-----//
| (___ | | / _ | |_ \-//
_|_ ___) |__| \_/ _|_ | // \
//-----\\
//---------\\
isugifNF/freebayes v1.0.0
----------------------------------------------------
Usage:
The typical command for running the pipeline is as follows:
nextflow run main.nf --fastaReference genomeFile.fasta --bam /full/path/input/file.bam --vcf outputPrefix -profile singularity,nova
Mandatory arguments:
--fastqs fastq files to run nanoplot on. (/data/*.fastq)
Optional arguments:
--help Display this help message
--outdir Specify output directory ('./out_dir')
--queueSize Max number of jobs submitted at one time (18)
--fasta-reference Input genome file to run freebayes on ("yourGenome.fasta")
--vcf Output VCF file name ("out.vcf")
--bam Bam input file ("In.bam")
--options Freebayes options ("--min-mapping-quality 0 --min-coverage 3 --min-supporting-allele-qsum 0 --ploidy 2 --min-alternate-fraction 0.2 --max-complex-gap 0")
--regionSize Size of the regions to split the file into (25000)
--windowSize size of windows to run freebayes on