git clone https://github.com/isugifNF/bwamem2.git
cd bwamem2
nextflow run main.nf --help
or
nextflow run isugifNF/bwamem2 -r main --help
N E X T F L O W ~ version 21.04.3
Launching `main.nf` [voluminous_hodgkin] - revision: 5d7eca7c21
Usage:
The typical command for running the pipeline is as follows:
nextflow run main.nf --genome GENOME.fasta --reads "*_{R1,R2}.fastq.gz" -profile singularity
Mandatory arguments:
--genome Genome fasta file, against which reads will be mapped to find SNPs
--reads Paired-end reads in fastq.gz format, will need to specify glob (e.g. "*_{R1,R2}.fastq.gz")
Optional configuration arguments:
-profile Configuration profile to use. Can use multiple (comma separated)
Available: local, slurm, singularity, docker [default:local]
--singularity_img Singularity image if [-profile singularity] is set [default:'shub://aseetharam/gatk:latest']
--docker_img Docker image if [-profile docker] is set [default:'j23414/gatk4']
--bwamem2_app Link to bwamem2 executable [default: 'bwa-mem2']
--samtools_app Link to samtools executable [default: 'samtools']
Optional other arguments:
--threads Threads per process [default:4 for local, 16 for slurm]
--window Window size passed to bedtools for gatk [default:100000]
--queueSize Maximum jobs to submit to slurm [default:20]
--account HPC account name for slurm sbatch, atlas and ceres requires this
--help