scRNA-seq with Cellranger fails at Seurat conversion stage

[FelixKrueger]

Description of the bug

We had a single-cell run that what used 4 sets of input files per sample (were using CellRanger in this case), here is an example:

Skin-M-48,s3://.../Skin-M-48_S1_L001_R1_001.fastq.gz,s3://.../Skin-M-48_S1_L001_R2_001.fastq.gz
Skin-M-48,s3://.../Skin-M-48_S2_L001_R1_001.fastq.gz,s3://.../Skin-M-48_S2_L001_R2_001.fastq.gz
Skin-M-48,s3://.../Skin-M-48_S3_L001_R1_001.fastq.gz,s3://.../Skin-M-48_S3_L001_R2_001.fastq.gz
Skin-M-48,s3://.../Skin-M-48_S4_L001_R1_001.fastq.gz,s3://.../Skin-M-48_S4_L001_R2_001.fastq.gz

The run then failed at the Seurat conversion due to file name collision:

Execution completed unsuccessfully!
The full error message was:

Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:MTX_TO_SEURAT (1)'

Caused by:
  Process `NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:MTX_TO_SEURAT` input file name collision -- There are multiple input files for each of the following file names: projection.csv, differential_expression.csv, barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, clusters.csv

Running the same command and the same files but with alevin as the aligner completes just fine.

Command used and terminal output

No response

Relevant files

No response

System information

Nextflow: 23.04.1 build 5866
nf-core/scrnaseq v2.3.2-g06a85e8

[adamrtalbot]

See #232, I think this fixes it.

[adamrtalbot]

Closed with #232