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description
Creates a .bai BAM index for the input BAM
outputs
{'bam_index': "A .bai BAM index associated with the input BAM. Filename will be basename(bam) + '.bai'."}

Inputs

Required

  • _runtime (Any, required)
  • bam (File, required): Input BAM format file to index

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=2); description: Number of cores to allocate for task; common: true
  • use_all_cores (Boolean, default=false); description: Use all cores? Recommended for cloud environments. Not recommended for cluster environments.; common: true

Outputs

  • bam_index (File)

merge

description
Merges multiple sorted BAMs into a single BAM
outputs
{'merged_bam': 'The BAM resulting from merging all the input BAMs'}

Inputs

Required

  • _runtime (Any, required)
  • bams (Array[File], required): An array of BAMs to merge into one combined BAM
  • prefix (String, required): Prefix for the BAM file. The extension .bam will be added.

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=2); description: Number of cores to allocate for task; common: true
  • use_all_cores (Boolean, default=false); description: Use all cores? Recommended for cloud environments. Not recommended for cluster environments.; common: true

Outputs

  • merged_bam (File)

sort

description
Sorts the input BAM file
outputs
{'sorted_bam': 'The input BAM after it has been sorted according to sort_order'}

Inputs

Required

  • _runtime (Any, required)
  • bam (File, required): Input BAM format file to sort

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=2): Number of cores to allocate for task
  • prefix (String, default=basename(bam,".bam") + ".sorted"): Prefix for the sorted BAM file. The extension .bam will be added.
  • queryname_sort (Boolean, default=false); description: If true, sort the BAM by queryname. If false, sort by coordinate.; common: true

Outputs

  • sorted_bam (File)

markdup

description
Marks duplicate reads in the input BAM file
outputs
{'duplicate_marked_bam': 'The input BAM with computationally determined duplicates marked.', 'duplicate_marked_bam_index': 'Index file for the duplicate marked BAM', 'markdup_log': 'Log file from the markdup process'}

Inputs

Required

  • _runtime (Any, required)
  • bam (File, required): Input BAM format file in which to mark duplicates

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=2): Number of cores to allocate for task
  • prefix (String, default=basename(bam,".bam")): Prefix for the markdup result files. The extensions markdup.bam will be added.
  • remove_duplicates (Boolean, default=false); description: If true, remove duplicates instead of marking them.; common: true

Outputs

  • duplicate_marked_bam (File)
  • duplicate_marked_bam_index (File)
  • markdup_log (File)

flagstat

description
Produces a report containing statistics about the alignments based on the bit flags set in the BAM
outputs
{'flagstat_report': 'sambamba flagstat STDOUT redirected to a file'}

Inputs

Required

  • _runtime (Any, required)
  • bam (File, required): Input BAM format file to generate flagstat for

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=2); description: Number of cores to allocate for task; common: true
  • outfile_name (String, default=basename(bam,".bam") + ".flagstat.txt"): Name for the flagstat report file
  • use_all_cores (Boolean, default=false); description: Use all cores? Recommended for cloud environments. Not recommended for cluster environments.; common: true

Outputs

  • flagstat_report (File)