Only UMAP for one sample in HTML report
Closed this issue · 2 comments
Operating System
Other Linux (please specify below)
Other Linux
No response
Workflow Version
prerelease
Workflow Execution
Command line
EPI2ME Version
No response
CLI command run
nextflow run epi2me-labs/wf-single-cell
-r prerelease
-w workspace
-profile singularity
--fastq ../fastq
--single_cell_sample_sheet samples.txt
--ref_genome_dir ~/10x/refdata-gex/refdata-gex-GRCh38-2020-A
--out_dir output
Workflow Execution - CLI Execution Profile
singularity
What happened?
I used a sample's CSV file passed with the --single_cell_sample_sheet option to the workflow. The workflow successfully produces the results in the output directory including 3 folders for each of the 3 samples. These folders also contain a umap folder with TSV files with UMAP coordinates for both gene and transcript. However, the HTML report wf-single-cell-report.html only includes a tab with an UMAPs for one sample. The same report contains in the section with knee and saturation plots tabs for all the samples. I am not sure if this is a bug or intended, so just in case submit this issue. I can see in report.py file in workflow_glue that the way tabs for samples are handled is different in the knee plot section than how it is done in the UMAP section. But I cannot tell whether there is a problem there.
Relevant log output
No errors were reported, and the workflow ran successfully.Application activity log entry
No response
Were you able to successfully run the latest version of the workflow with the demo data?
yes
Other demo data information
No response
This is a known bug that will be fixed in the next release.
OK thanks. Great to know!