Closed Coracollar closed 1 month ago
nrhorner
commented
1 month ago Hi @Coracollar
The troubleshooting section mentions this issue: https://github.com/epi2me-labs/wf-single-cell?tab=readme-ov-file#troubleshooting.
Could you try following the suggestion there please?
Coracollar
commented
1 month ago Hello Neil, Which nexflow.config should I change? Because I created a config file in the configs/confs directory and then added it to nfcore_custom.config, but the workflow seems to refuse to use any custom config claiming it does not exist (even the ones that are already there like wehi). Then I tried to modify the nextflow.config inside the v2_1_0 directory adding runOptions = '--writable-tmpfs' in the singularity profile: Like in here:
profiles {
// the "standard" profile is used implicitely by nextflow
// if no other profile is given on the CLI
standard {
docker {
enabled = true
// this ensures container is run as host user and group, but
// also adds host user to the within-container group
runOptions = "--user \$(id -u):\$(id -g) --group-add 100"
}
}
// using singularity instead of docker
singularity {
singularity {
enabled = true
autoMounts = true
runOptions = '--writable-tmpfs'
}
}Then I ran the pipeline again and had the exact same error.
Is there any other config files hidden? Do you know why the pipeline might be ignoring the custom config even when they were downloaded? Cheers, Cora
nrhorner
commented
1 month ago Hi @Coracollar
Just create a a new config file anywhere that is readable, and point the workflow to it using -c path/to/config
The workflow log should indicate whic config files are being used for a run, for example:
|||||||||| | ____| _ \_ _|___ \| \/ | ____| | | __ _| |__ ___
||||| | _| | |_) | | __) | |\/| | _| _____| |/ _` | '_ \/ __|
||||| | |___| __/| | / __/| | | | |__|_____| | (_| | |_) \__ \
|||||||||| |_____|_| |___|_____|_| |_|_____| |_|\__,_|_.__/|___/
|||||||||| wf-single-cell v2.3.0
--------------------------------------------------------------------------------
Core Nextflow options
...
configFiles : /Users/user/.nextflow/config, /Users/user/git/workflows/wf-single-cell/nextflow.configHi @Coracollar Did you have any luck with this?
Coracollar
commented
4 weeks ago Hi sorry for the late reply, no luck. Same problem, same error. I've given up using epi2me and changed to flames.
On Tue, Oct 22, 2024 at 3:25 AM Neil Horner @.***> wrote:
Hi @Coracollar https://github.com/Coracollar Did you have any luck with this?
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Operating System
CentOS 7
Other Linux
No response
Workflow Version
v 2.1.0, 2.2.0, 2.3.0
Workflow Execution
Command line (Local)
Other workflow execution
No response
EPI2ME Version
No response
CLI command run
nextflow run tools/epi2me-labs-wf-single-cell_v2.1.0/v2_1_0/ \ --expected_cells 100 \ --fastq 'wf-single-cell-demo/chr17.fq.gz' \ --kit '3prime:v3' \ --ref_genome_dir 'wf-single-cell-demo' \ --genes_of_interest 'wf-single-cell-demo/umap_plot_genes.csv' \ -profile singularity \ --threads 4
Workflow Execution - CLI Execution Profile
None
What happened?
I have tried several versions of the workflow, downloading them with nfcore download and downloading the singularity image and in all of them I have the same error running the test command. There seems to be an error with numba that is killing the workflow, I have tried to install different numba versions but it does not solve it. Any idea?
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