Footprint calling pipeline

Nextflow wrapper for footprint-tools (https://footprint-tools.readthedocs.io/en/latest/)

Requirements

• Nextflow (https://www.nextflow.io/)
• conda (https://docs.conda.io/en/latest/)

Usage

1. Create conda environment from environment.yml file or use the existing one
2. Modify nextflow.config to computing enviroment specifications
3. Fill in params paths in params.config. You can also specify parameters in command line. Please find detailed explanation of the parameters in the Config section.
4. Run the pipeline with nextflow run main.nf -profile Altius

Config

There are two config files in the repository.

• nextflow.config - contains enviornment configuration. Detailed explanation can be found at https://www.nextflow.io/docs/latest/config.html.
• params.config - specifies paths to input files.

Following parameters should be present in params.config. Each option can be specified either in params.config file or with a command line.

• outdir - directory to save results into. May be a relative path.

• conda - path to installed conda (from environment.yml)

• samples_file - tab-delimited file with metadata for samples. The file must contain a header and the following columns (other columns are permitted and ignored)

  • ag_id - unique identifier of the sample.
  • filtered_alignments_bam - path to a bam/cram file
  • bam_index - index to the bam/cram file, if not provided look for index at ${filtered_alignments_bam}.crai
  • hotspot_peaks_point1per - path to peaks called with hotspot2

• genome_fasta_file - path to genome fasta