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Snakefile Post Processing
Workflow doing quality control steps and creation of ReMap like file containing all peaks from peakcalling results. As quality control for ChIP-seq/DAP-seq is different than quality control for ChIP-exo two workflows exist.
This workflow use the outputs created by Snakefile ReMap v4. It also needs summary tab files created for Snakefile ReMap v4 (see here how to create them).
To run workflow:
For slurm
snakemake (--use-singularity|--use-conda) --singularity-args "-B /path/to/working_directory:/path/to/working_directory" --snakefile 2.scripts/snakefiles_workflow/Snakefile_remap_post_processing.py --cluster-config 2.scripts/cluster_configuration/EXAMPLE_cluster_slurm.json --cluster "sbatch --job-name {cluster.job-name} -p {cluster.partition} --ntasks {cluster.ntasks} --cpus-per-task={cluster.thread} -o {cluster.stdout} -e {cluster.stderr} --time {cluster.time} --mem-per-cpu={cluster.memory} " --configfile 2.scripts/snakemake_configuration/EXAMPLE_Snakefile_config_remap.json --resources res=150 --cores X
For Torque
snakemake (--use-singularity|--use-conda) --snakefile 2.scripts/snakefiles_workflow/Snakefile_remap_post_processing.py --printshellcmds --cores X --cluster-config 2.scripts/cluster_configuration/EXAMPLE_cluster_torque.json --cluster "qsub -V -q {cluster.queue} -l nodes={cluster.node}:ppn={cluster.thread} -o {cluster.stdout} -e {cluster.stderr}" --configfile 2.scripts/snakemake_configuration/EXAMPLE_Snakefile_config_remap.json --use-conda