Launching Analysis

Overview

Run on DRAGEN Server

The pipeline is launched with the bash script called run_DRAGEN_Solid_WGS_TN_4.4.4.sh, which is installed in the /usr/local/bin directory. The bash script is executed on the command line and runs the software with Docker or Apptainer (formerly Singularity). For command-line options, refer to Command Line Options page in user guide for details.

By default, analysis output is written to the /staging/DRAGEN_Solid_WGS_TN_4.4.4_Analysis_ directory. To write to a different output directory, run the bash script with the following argument

  --analysisFolder <FULL_PATH_TO_ANALYSIS_FOLDER>

Do not move files when the analysis is running. Moving files during the analysis can cause the analysis to fail or provide incorrect results.

An analysis can start from a sequencing system run folder containing BCL files or from one or more input folders containing FASTQ, BAM or CRAM files. A sample sheet value is also a valid argument. The following requirements apply to each:

If launching an analysis from a run folder, specify the following argument and path:

  --runFolder <FULL_PATH_TO_RUN_FOLDER>

By default, the software uses the SampleSheet.csv in the provided path.

If launching an analysis from one or more input folders, specify the following argument and path:

  --inputFolders <COMMA_SEPARATED_FULL_PATH_TO_INPUT_FOLDERS> --inputType [BAM|CRAM|FASTQ]

By default, the software uses the SampleSheet.csv in the provided path.

The default sample sheet can be overwritten by providing the argument:

  --sampleSheet <FULL_PATH_TO_A_SAMPLE_SHEET_FILE>

Common use cases

1. Wait for any running pipeline containers to complete before launching a new analysis. Run the following command to generate a list of running containers:docker ps

2. Select from one of the following options:

• Start from BCL files in the run folder with the sample sheet included in the run folder. DRAGEN_Solid_WGS_TN_4.4.4.sh \ --runFolder /staging/{RunFolderName} \ --analysisFolder /staging/{AnalysisFolderName}

• Start from BCL files in the run folder with the sample sheet located in a folder other than the run folder. DRAGEN_Solid_WGS_TN_4.4.4.sh \ --runFolder /staging/{RunFolderName} \ --analysisFolder /staging/{AnalysisFolderName} \ --sampleSheet /staging/{SampleSheetName}.csv

• Start from BCL files in the run folder with a different sample sheet and demultiplexing only. DRAGEN_Solid_WGS_TN_4.4.4.sh \ --runFolder /staging/{RunFolderName} \ --analysisFolder /staging/{AnalysisFolderName} \ --sampleSheet /staging/{SampleSheetName}.csv \ --demultiplexOnly

• Start from FASTQ with the sample sheet included in the FASTQ folder and with different resources and hash table folders. DRAGEN_Solid_WGS_TN_4.4.4.sh \ --resourcesFolder /staging/illumina/DRAGEN_TSO500/resources \ --hashtableFolder /staging/illumina/DRAGEN_TSO500/ref_hashtable \ --fastqFolder /staging/{FastqFolderName} \ --analysisFolder /staging/{AnalysisFolderName}

• Start from FASTQ folder with sample sheet included in the FASTQ folder and subset of samples or pairs. DRAGEN_Solid_WGS_TN_4.4.4.sh \ --fastqFolder /staging/{FastqFolderName} \ --analysisFolder /staging/{AnalysisFolderName} \ --sampleOrPairIDs "Pair_1,Pair2"