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fastqc

description
Generates a FastQC quality control metrics report for the input BAM file
outputs
{'raw_data': 'A zip archive of raw FastQC data. Can be parsed by MultiQC.', 'results': 'A gzipped tar archive of all FastQC output files'}

Inputs

Required

  • _runtime (Any, required)
  • bam (File, required): Input BAM format file to run FastQC on

Defaults

  • 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.
  • ncpu (Int, default=4); description: Number of cores to allocate for task; common: true
  • prefix (String, default=basename(bam,".bam") + ".fastqc_results"): Prefix for the FastQC results directory. The extension .tar.gz will be added.
  • use_all_cores (Boolean, default=false); description: Use all cores? Recommended for cloud environments.; common: true

Outputs

  • raw_data (File)
  • results (File)