Cell Ranger

This WDL file wrap the 10x Genomics Cell Ranger tool. Cell Ranger is a tool for handling scRNA-Seq data.

count

description
This WDL task runs Cell Ranger count to generate an aligned BAM and feature counts from scRNA-Seq data.
outputs
{'bam': 'Aligned BAM file', 'bam_index': 'BAM index file', 'qc': 'Quality control metrics in CSV format', 'barcodes': 'Barcodes in gzipped TSV format', 'features': 'Filtered features in gzipped TSV format', 'matrix': 'Filtered matrix of features', 'filtered_gene_h5': 'Filtered gene matrix in H5 format', 'raw_gene_h5': 'Raw gene matrix in H5 format', 'raw_barcodes': 'Raw barcodes in gzipped TSV format', 'raw_features': 'Raw features in gzipped TSV format', 'raw_matrix': 'Raw matrix of features', 'mol_info_h5': 'Molecule information in H5 format', 'web_summary': 'HTML summary of the run', 'cloupe': 'Cloupe file for visualization'}

Inputs

Required

  • _runtime (Any, required)
  • fastqs_tar_gz (File, required): Path to the FASTQ folder archive in .tar.gz format
  • id (String, required): A unique run ID
  • transcriptome_tar_gz (File, required): Path to Cell Ranger-compatible transcriptome reference in .tar.gz format

Defaults

  • memory_gb (Int, default=16): 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
  • use_all_cores (Boolean, default=false): Use all cores? Recommended for cloud environments.

Outputs

  • bam (File)
  • bam_index (File)
  • qc (File)
  • barcodes (File)
  • features (File)
  • matrix (File)
  • filtered_gene_h5 (File)
  • raw_gene_h5 (File)
  • raw_barcodes (File)
  • raw_features (File)
  • raw_matrix (File)
  • mol_info_h5 (File)
  • web_summary (File)
  • cloupe (File)

bamtofastq

description
This WDL task runs the 10x bamtofastq tool to convert Cell Ranger generated BAM files back to FASTQ files
outputs
{'fastqs': 'FASTQ files', 'fastqs_archive': 'FASTQ files in a tarball', 'read_one_fastq_gz': 'Read 1 FASTQ files', 'read_two_fastq_gz': 'Read 2 FASTQ files'}

Inputs

Required

  • _runtime (Any, required)
  • bam (File, required): Input BAM to convert to Cell Ranger compatible fastqs

Defaults

  • cellranger11 (Boolean, default=false): Convert a BAM produced by Cell Ranger 1.0-1.1
  • gemcode (Boolean, default=false): Convert a BAM produced from GemCode data (Longranger 1.0 - 1.3)
  • longranger20 (Boolean, default=false): Convert a BAM produced by Longranger 2.0
  • memory_gb (Int, default=40): 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
  • use_all_cores (Boolean, default=false): Use all cores? Recommended for cloud environments.

Outputs

  • fastqs (Array[File])
  • fastqs_archive (File)
  • read_one_fastq_gz (Array[File])
  • read_two_fastq_gz (Array[File])