Launching Analysis
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The Heme pipeline is launched with the bash script called DRAGEN_Heme_WGS-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 for details.
By default, analysis output is written to the /staging/DRAGEN_Heme_WGS_4.4.4_Analysis_ directory. To write to a different output directory, run the bash script with the following argument
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:
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:
By default, the software uses the SampleSheet.csv in the provided path.
The default sample sheet can be overwritten by providing the argument:
Wait for any running Heme pipeline containers to complete before launching a new analysis. Run the following command to generate a list of running containers:docker ps
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_Heme_WGS_TO_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_Heme_WGS_TO_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_Heme_WGS_TO_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_Heme_WGS_TO_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_Heme_WGS_TO_4.4.4.sh \
--fastqFolder /staging/{FastqFolderName} \
--analysisFolder /staging/{AnalysisFolderName} \
--sampleOrPairIDs "Pair_1,Pair2"