Closed MaestSi closed 5 months ago
Based on the message at the beginning of the log I would say you are not running 1.1.0 (41eceabbd7) but version 0.2.7 (9272e2ce6d). How did you update to the latest version? I have had this problem in the past. You can pull the latest version using nextflow
:
nextflow pull epi2me-labs/wf-single-cell
You could also do it using git if you know the location of the assets. In my system is ~/.nextflow/assets/epi2me-labs/wf-single-cell/
. Going to that folder and running git pull
also retrieves the latest version. I am not sure if there is an advantage between using nextflow or git directly.
Thanks for the advice, I just cloned the new repository and was expecting it to be updated automatically. My fault, after running
nextflow pull epi2me-labs/wf-single-cell
the pipeline completes successfully on demo data. I still have an issue with my own dataset, but I'll open a separate issue for that one.
Thanks,
Simone
Operating System
Other Linux (please specify below)
Other Linux
Ubuntu 20.04
Workflow Version
v1.1.0
Workflow Execution
Command line
EPI2ME Version
No response
CLI command run
nextflow run epi2me-labs/wf-single-cell --fastq ./wf-single-cell-demo/chr17.fq.gz --kit_name 3prime --kit_version v3 --expected_cells 100 --ref_genome_dir ./wf-single-cell-demo/ --plot_umaps -profile singularity
Workflow Execution - CLI Execution Profile
singularity
What happened?
I just updated the workflow to version 1.1.0. However, after updating, it seems I cannot complete a run, not even on the test dataset.
Relevant log output
Application activity log entry
No response
Were you able to successfully run the latest version of the workflow with the demo data?
no
Other demo data information
No response