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rnaseq

description
Generates runs QualiMap's rnaseq tool on the input BAM file. Note that we don't expose the -p parameter. This is used to set strandedness protocol of the sample, however in practice it only disables certain calculations. We do not expose the parameter so that the full suite of calculations is always performed.
outputs
{'raw_summary': "Raw text summary of QualiMap's results. Can be parsed by MultiQC.", 'raw_coverage': "Raw text of QualiMap's coverage analysis results. Can be parsed by MultiQC.", 'results': 'Gzipped tar archive of all QualiMap output files'}

Inputs

Required

  • _runtime (Any, required)
  • bam (File, required): Input BAM format file to run qualimap rnaseq on
  • gtf (File, required): GTF features file. Gzipped or uncompressed.

Defaults

  • memory_gb (Int, default=16): RAM to allocate for task
  • 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.
  • name_sorted (Boolean, default=false); description: Is the BAM name sorted? QualiMap has an inefficient sorting algorithm. In order to save resources we recommend collating your input BAM before QualiMap and setting this parameter to true.; common: true
  • paired_end (Boolean, default=true); description: Is the BAM paired end?; common: true
  • prefix (String, default=basename(bam,".bam") + ".qualimap_rnaseq_results"): Prefix for the results directory and output tarball. The extension .qualimap_rnaseq_results.tar.gz will be added.

Outputs

  • raw_summary (File)
  • raw_coverage (File)
  • results (File)

bamqc

description
[Deprecated] This WDL task runs QualiMap's bamqc tool on the input BAM file. This task has been deprecated due to memory leak issues. Use at your own risk, for some samples can consume over 1TB of RAM.
deprecated
true

Inputs

Required

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

Defaults

  • memory_gb (Int, default=32): RAM to allocate for task, specified in GB
  • 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=1): Number of cores to allocate for task
  • prefix (String, default=basename(bam,".bam")): Prefix for the file. The extension <extension> will be added.
  • use_all_cores (Boolean, default=false): Use all cores? Recommended for cloud environments.

Outputs

  • results (File)