nrhorner
commented
1 year ago Hi @ddiez
Sorry, the workflow is giving you an incorrect error message.
I think the issue is because the sample_ids do no match between the single_cell_sample_sheet and those that are determined by the input data.
doing --fastq wf-single-cell-demo/fastq/A/chr17a.fq.gz means the input from the A folder will have a sample_id of chr17 .
But if you do --fastq wf-single-cell-demo/fastq/A that should set the sample_id to 'A' the same as in your sample_sheet.
you might want to put your sample data in subdirectories with each one named with the sample_id
fastq
├── A
│ └── reads.fq
└── B
└── reads.fq
ddiez
Operating System
Other Linux (please specify below)
Other Linux
Ubuntu 23.04
Workflow Version
v0.2.7-g9272e2c
Workflow Execution
Command line
EPI2ME Version
No response
CLI command run
nextflow run epi2me-labs/wf-single-cell \ -w single-cell-demo-out2/workspace \ -profile standard \ --fastq wf-single-cell-demo/fastq/A/chr17a.fq.gz wf-single-cell-demo/fastq/B/chr17b.fq.gz \ --single_cell_sample_sheet samples.txt \ --ref_genome_dir ~/10x/refdata-gex/refdata-gex-GRCh38-2020-A \ --out_dir single-cell-demo-out2 \ --plot_umaps \ --umap_n_repeats 1
Workflow Execution - CLI Execution Profile
standard (default)
What happened?
I am trying to use single_cell_sample_sheet option to pass the information of three different samples. To test this, I am using the demo dataset and pretending I have to samples. I provide the sample information in a samples.txt file that contains the following information:
When I run the workflow using the code paste above, I get the following error:
The full log is included below. It seems the single_cell_sample_sheet file is correctly detected. For some reason the pipeline fails when checking the kit is one of the supported kits. Looking at the code in main.nf it is not clear to me why this might be. So I am wondering if I am using this option correctly or there is a problem in the workflow.
Relevant log output
Application activity log entry
No response