command not found issue

[mlesche]

Dear nf-core Team,

I'm trying to run the pipeline but struggling already in the first bit of the code. My command is:
#nextflow run /nfcore/atacseq/ -c dcgc.config -with-singularity /singularity/atacseq_latest.sif --genome mm10 --design design.csv

And the error is as follows:

[0;35m[nf-core/atacseq] Pipeline completed with errors
Adieu
Error executing process > 'reformat_design (design.csv)'

Caused by:
Process reformat_design (design.csv) terminated with an error exit status (127)

Command executed:

reformat_design.py design.csv design_reformat.csv

Command exit status:
127

Command output:
(empty)

Command error:
WARNING: seccomp requested but not enabled, seccomp library is missing or too old
.command.sh: line 2: reformat_design.py: command not found

Work dir:
/projects/seq-work/analysis/development/atac/work/d6/8629a0d1713f3813290de65e9db660

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

I don't understand the error because it says that ".command.sh: line 2: reformat_design.py: command not found". This python script exists and I can run it on my own with out any problems but it is not being picked up by the by the nextflow command. Secondly I'm worried about "WARNING: seccomp requested but not enabled, seccomp library is missing or too old"

Can you help me with that?

Thanks

[drpatelh]

Hi @mlesche! I have literally just seen this issue! Any pipeline issues should be posted here and not on my fork which is why I missed it. Sorry!

I realise its quite a time ago now but did you manage to sort this out?