peak_calling
Ready to use Nextflow paired reads peaks calling workflow available on genotoul /work/project/lpgp/Nextflow/peak_calling.
Usage example
#!/bin/bash
module load system/singularity-3.7.3
module load bioinfo/Nextflow-v21.04.1
nextflow run /work/project/lpgp/Nextflow/peak_calling/ \
-profile slurm \
--input "/work/project/lpgp/CHIP/design.csv" \
--gsize 2.34167e+09 \
--qvalue 0.05 \
--out_dir "${PWD}/results/"
#!/bin/bash
module load system/singularity-3.7.3
module load bioinfo/Nextflow-v21.04.1
nextflow run /work/project/lpgp/Nextflow/peak_calling/ \
-profile slurm \
-resume \
--input "/work/project/lpgp/Spermaheat/design.csv" \
--skip_plotfingerprint \
--skip_bamcoverage \
--ATAC \
--gsize 2.34167e+09 \
--qvalue 0.05 \
--broad \
--broad_cutoff 0.1 \
--out_dir "${PWD}/results"Install flow and build singularity image
Clone peak_calling git and build local singularity image (with system admin) based on the provided singularity definition file.
git clone https://forgemia.inra.fr/lpgp/peak_calling.git
sudo singularity build ./peak_calling/singularity/peak_calling.sif ./genome_aln/singularity/peak_calling.def