Updates to the Fastq generation and QC pipelines and supporting functions, for compatibility with Cellranger 8.0.0.
Significant changes in Cellranger 8.0.0 which need to be accommodated in the QC pipeline are:
cellranger count now has a required --create-bam command line option, which must be set to either true or false. Recommended default is true (i.e. BAM file will be created) if unsure;
cellranger multi replaces the no-bam configuration option with a new create-bam option (which is essentially the same as the --create-bam command line option for count)
The multi config template generation code has therefore been updated to take the target Cellranger version as optional input; the setup_analysis_dirs command supplies the version from the processing pipeline when generating templates (which should be consistent in most cases).
There is also a minor change to the per-sample metrics.csv files produced by 8.0.0 compared to earlier versions, in that 8.0.0 no longer outputs a median_reads_per_cell value (which is currently reported as part of the QC reporting); the mean_reads_per_cell value will be reported instead for version 8.0.0.
Finally, although this PR implements compatibility with Cellranger 8.0.0, the default version for testing remains at 7.1.0.
Updates to the Fastq generation and QC pipelines and supporting functions, for compatibility with Cellranger 8.0.0.
Significant changes in Cellranger 8.0.0 which need to be accommodated in the QC pipeline are:
cellranger countnow has a required--create-bamcommand line option, which must be set to eithertrueorfalse. Recommended default istrue(i.e. BAM file will be created) if unsure;cellranger multireplaces theno-bamconfiguration option with a newcreate-bamoption (which is essentially the same as the--create-bamcommand line option forcount)Creating BAM files will produce larger overall output sizes and can also result in longer compute times, but may not be particularly advantageous in all cases, specifically for Flex datasets it is recommended to disable BAM file creation (see https://kb.10xgenomics.com/hc/en-us/articles/24292856143885-Understanding-the-create-bam-Parameter-in-Cell-Ranger-v8-0).
The multi config template generation code has therefore been updated to take the target Cellranger version as optional input; the
setup_analysis_dirscommand supplies the version from the processing pipeline when generating templates (which should be consistent in most cases).There is also a minor change to the per-sample
metrics.csvfiles produced by 8.0.0 compared to earlier versions, in that 8.0.0 no longer outputs amedian_reads_per_cellvalue (which is currently reported as part of the QC reporting); themean_reads_per_cellvalue will be reported instead for version 8.0.0.Finally, although this PR implements compatibility with Cellranger 8.0.0, the default version for testing remains at 7.1.0.