Configuration for fastq_screen

The database configuration for fastq_screen can be found in workflow/config/fastq_screen_slurm.conf. Bowtie2 indexes for different species were created upfront and the absolute path with prefix of the index are provided. You can modify the file based on your need.

Configuration for kraken2

Three files below are used as database for kraken2: 

hash.k2d
opts.k2d
taxo.k2d

Please change the path of kraken2db in workflow/config/program.py.

Configuration for HPC

You need to modify the singularity-args and default-resources parameters in workflow/profile/slurm/config.v8+.yaml according to the required storage space and partition details.

To customize the workflow/profile/slurm/config.v8+.yaml file for your specific storage and partition requirements, modify the singularity-args and default-resources parameters as needed.

  1. singularity-args: Adjust this to specify the necessary bind paths for your workflow. These paths should point to storage locations on your system. For example:
singularity-args: ' "--cleanenv --no-home -B /scratch/ccrsf_scratch -B /mnt/ccrsf-static -B /mnt/ccrsf-ifx -B /mnt/ccrsf-raw -B /mnt/ccrsf-active" '
  • --cleanenv: Ensures a clean environment within the container.
  • --no-home: Disables binding of the home directory.

  • -B : Specifies bind paths for directories required by your workflow.

  • default-resources: Adjust these parameters to reflect your job's runtime, memory, disk space, and SLURM partition requirements.

default-resources:
  runtime: 7200             # Maximum runtime in seconds (2 hours)
  mem_mb: 100000            # Memory allocation in MB (100 GB)
  disk_mb: 1000000          # Disk space allocation in MB (1 TB)
  slurm_partition: "norm"   # Target SLURM partition

Be sure to align these settings with the actual storage paths and resource quotas for your computing environment.