Issue running v1.1.0 on demo dataset
Closed this issue · 2 comments
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
N E X T F L O W ~ version 23.10.1
NOTE: Your local project version looks outdated - a different revision is available in the remote repository [41eceabbd7]
Launching `https://github.com/epi2me-labs/wf-single-cell` [happy_brattain] DSL2 - revision: 9272e2ce6d [master]
WARN: Found unexpected parameters:
* --full_length_only: true
- Ignore this warning: params.schema_ignore_params = "full_length_only"
|||||||||| _____ ____ ___ ____ __ __ _____ _ _
|||||||||| | ____| _ \_ _|___ \| \/ | ____| | | __ _| |__ ___
||||| | _| | |_) | | __) | |\/| | _| _____| |/ _` | '_ \/ __|
||||| | |___| __/| | / __/| | | | |__|_____| | (_| | |_) \__ \
|||||||||| |_____|_| |___|_____|_| |_|_____| |_|\__,_|_.__/|___/
|||||||||| wf-single-cell v1.1.0-g9272e2c
--------------------------------------------------------------------------------
Core Nextflow options
revision : master
runName : happy_brattain
containerEngine : singularity
container : [withLabel:singlecell:ontresearch/wf-single-cell:sha8e7d91013029ea8721743bd087583e5205cdc1dc, withLabel:wf_common:ontresearch/wf-common:sha2816439fd5aa81902836ea5794447b54947fa056]
launchDir : /mnt/home/maestri/pipelines/wf-single-cell
workDir : /mnt/home/maestri/pipelines/wf-single-cell/work
projectDir : /mnt/home/maestri/.nextflow/assets/epi2me-labs/wf-single-cell
userName : maestri
profile : singularity
configFiles : /mnt/home/maestri/.nextflow/assets/epi2me-labs/wf-single-cell/nextflow.config, /mnt/home/maestri/pipelines/wf-single-cell/nextflow.config
Input Options
fastq : ./wf-single-cell-demo/chr17.fq.gz
ref_genome_dir : ./wf-single-cell-demo/
expected_cells : 100
Output Options
plot_umaps : true
Advanced options
matrix_min_genes: 200
umap_n_repeats : 3
!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-single-cell for your analysis please cite:
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
--------------------------------------------------------------------------------
This is epi2me-labs/wf-single-cell v1.1.0-g9272e2c.
--------------------------------------------------------------------------------
ERROR ~ Argument of `file` function cannot be null
-- Check script '/mnt/home/maestri/.nextflow/assets/epi2me-labs/wf-single-cell/main.nf' at line: 284 or see '.nextflow.log' file for more details
(nextflow_env) maestri@scrapper:~/pipelines/wf-single-cell$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 20.04.2 LTS
Release: 20.04
Codename: focalApplication 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
Based on the message at the beginning of the log I would say you are not running 1.1.0 (41eceab) but version 0.2.7 (9272e2c). 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