snareseq2-v2.0.yaml

files:
  -
    pattern: extras\/.*
    required: True
    description: Folder for general lab-specific files related to the dataset.
  -
    pattern: extras\/expected_cell_count\.txt
    required: False
    description: The expected cell count for the RNA sequencing dataset. This is an optional file that, if present, will be used by the HIVE's RNA sequencing analysis pipeline. With some datasets, knowing the expected cell count has improved the output of the HIVE analysis pipeline.
  -
    pattern: raw\/.*
    required: True
    description: All raw data files for the experiment.
  -
    pattern: raw\/fastq\/.*
    required: True
    description: Raw sequencing files for the experiment.
  -  
    pattern: raw\/fastq\/RNA\/.*
    required: True
    description: Directory containing fastq files pertaining to RNAseq sequencing.
  -
    pattern: raw\/fastq\/RNA\/[^\/]+_R[^\/]+\.fastq\.gz
    required: True
    description: This is a GZip'd version of the forward and reverse fastq files from RNAseq sequencing (R1 and R2).
    is_qa_qc: False
  -  
    pattern: raw\/fastq\/ATAC\/.*
    required: True
    description: Directory containing fastq files pertaining to ATACseq sequencing.
  -
    pattern: raw\/fastq\/ATAC\/[^\/]+_R[^\/]+\.fastq\.gz
    required: True
    description: This is a GZip'd version of the fastq files containing the forward, reverse and barcode reads from ATACseq sequencing (R1, R2 and R3). Further, if the barcodes are in R3 (as with 10X) then the metadata field "barcode reads" would be set to "Read 2 (R2)" and the fastq file named "*_R2*fastq.gz" would be expected.
    is_qa_qc: False
  -
    pattern: lab_processed\/.*
    required: False
    description: Experiment files that were processed by the lab generating the data.