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coverage

description
Runs the Mosdepth tool for calculating coverage
outputs
{'summary': 'A summary of mean depths per chromosome and within specified regions per chromosome', 'global_dist': 'The $prefix.mosdepth.global.dist.txt file contains a cumulative distribution indicating the proportion of total bases that were covered for at least a given coverage value. It does this for each chromosome, and for the whole genome.', 'region_dist': 'The $prefix.mosdepth.region.dist.txt file contains a cumulative distribution indicating the proportion of total bases in the region(s) defined by coverage_bed that were covered for at least a given coverage value'}

Inputs

Required

  • _runtime (Any, required)
  • bam (File, required): Input BAM format file to calculate coverage for
  • bam_index (File, required): BAM index file corresponding to the input BAM

Optional

  • coverage_bed (File?): BED file to pass to the -b flag of mosdepth. This will restrict coverage analysis to regions defined by the BED file.

Defaults

  • min_mapping_quality (Int, default=20); description: Minimum mapping quality to pass to the -Q flag of mosdepth; common: true
  • modify_disk_size_gb (Int, default=0): Add to or subtract from dynamic disk space allocation. Default disk size is determined by the size of the inputs. Specified in GB.
  • prefix (String, default=basename(bam,".bam")): Prefix for the mosdepth report files. The extensions .mosdepth.summary.txt, .mosdepth.global.dist.txt and .mosdepth.region.dist.txt will be added.
  • use_fast_mode (Boolean, default=true): Use Mosdepth's 'fast mode'? This enables the -x flag.

Outputs

  • summary (File)
  • global_dist (File)
  • region_dist (File?)