2. Usage


2.1. Preparation of sample data

bgrr| takes as input a set of paired-end libraries, which need to be passed to the pipeline in form of a samplesheet. This samplesheet needs to be comma-separated and can be either generated manually (s. below for column format) or with the included create_samplesheet script. The script takes as argument a directory containing the fastq files (currently with mandatory .fastq.gz suffix) and writes the samplesheet to stdout.

Example usage

create_samplesheet <read_directory> > samplesheet.csv

For manual generation of the samplesheet, please create a comma-separated file following the column order below. Please note that items have to be present unless noted otherwise.

  1. Sample ID
  2. Sample Name (can be the same as Sample ID; the intention is to allow a more understandable sample reference in the future)
  3. Full path to R1 file
  4. Full path to R2 file
  5. LEAVE EMPTY (intended use: Full path to single-end file)
  6. LEAVE EMPTY (intended use: NCBI taxonomy id)
  7. LEAVE EMPTY (intended use: Taxonomy name)
  8. LEAVE EMPTY (intended use: FastQC report for raw R1)
  9. LEAVE EMPTY (intended use: FastQC report for raw R2)
  10. LEAVE EMPTY (intended use: FastQC report for raw single-end file)

Please note that despite columns 5-10 not being used, bgrr| still expects to see 10 columns at present.

2.2. Preparation of the bgrr| run

bgrr| runs are driven by two configuration files, which need to be adapted to your computing environment. Templates are included in the bgrrl/etc directory in the bgrr| source directory. To copy these files to the current run you can use the bginit command. bginit -o <outdir> will automatically copy the files into the folder <outdir>/config. The copies can then be edited.

2.2.1. bgrrl_config.yaml

2.2.2. hpc_config.json