Have you checked the docs?
Description of the bug
When running CMO samples in nf-core/scrnaseq pipeline, the module fails with the following:
cat > cellranger_multi_config.csv <<-CONFIG_EOF
[gene-expression]
reference,$PWD/references/gex/GRCh38
probe-set,$PWD/references/gex/probeset/frna_probeset_subset.csv
chemistry,auto
create-bam,true
[libraries]
fastq_id,fastqs,lanes,feature_types
PBMC_10K_CMO,$PWD/fastq_all/gex,,Gene Expression
PBMC_10K_CMO,$PWD/fastq_all/cmo,,Multiplexing Capture
[samples]
$(cat references/cmo/barcodes/PBMC_10K_CMO_cmo.csv)
CONFIG_EOF
cellranger multi
--id=PBMC_10K_CMO
--csv=cellranger_multi_config.csv
--localcores=4
--localmem=10 \
Command exit status:
1
Command output:
Martian Runtime - v4.0.14
Serving UI at [http://10707875421d:36439?auth=7OJWhXpSxQvRatJNYv0SjocGgtUNWPRpaXYAV_c5v6s](http://10707875421d:36439/?auth=7OJWhXpSxQvRatJNYv0SjocGgtUNWPRpaXYAV_c5v6s)
Running preflight checks (please wait)...
[error] Pipestance failed. Error log at:
PBMC_10K_CMO/SC_MULTI_CS/MULTI_PREFLIGHT/fork0/chnk0-u00b97425c3/_errors
Log message:
These library types are not compatible with Flex: Multiplexing Capture
The problem is that, when using Multiplexing Capture, the probe-set reference should not be added in the config.
The solution
The required change in the module is very simple, changing this line from:
if (gex_frna_probeset) gex_section << "probe-set,\$PWD/${gex_frna_probeset.name}"
to
// still allow frna probe-set for flex, but avoid adding when CMO or OCM barcodes are present, since those are mutually exclusive with frna
if (gex_frna_probeset && !has_cmo && !has_ocm) gex_section << "probe-set,\$PWD/${gex_frna_probeset.name}"
Command used and terminal output
Relevant files
No response
System information
No response
Have you checked the docs?
Description of the bug
When running CMO samples in
nf-core/scrnaseqpipeline, the module fails with the following:The problem is that, when using Multiplexing Capture, the probe-set reference should not be added in the config.
The solution
The required change in the module is very simple, changing this line from:
to
Command used and terminal output
Relevant files
No response
System information
No response