ValueError: empty separator (splitchar)

[husensofteng]

Hi,
When I run the pipeline for a customised database including variant peptides and others, I get the error below.

It seems the splitchar variable in label_sub_pos.py is not handled properly. In cases where no saavheader is assigned in ipaw.nf, the python script is still called but without passing the splitchar variable although used in the script.

ERROR nextflow.processor.TaskProcessor - Error executing process > 'prepSpectrumAI (1)'

Caused by:
Process prepSpectrumAI (1) terminated with an error exit status (1)

Command executed:

python3 /pgpython/label_sub_pos.py --input_psm setA_variant_psmtable.txt --output specai_in.txt --splitchar ""

Command exit status:
1

Command output:
(empty)

Command error:
Traceback (most recent call last):
File "/pgpython/label_sub_pos.py", line 50, in
splitheader = acc.split(splitchar)[-1]
ValueError: empty separator
.command.stub: line 99: 11 Terminated nxf_trace "$pid" .command.trace

[yafeng]

I see, maybe i can set a default value here in case it is not provided from the input by --splitchar

[husensofteng]

that works, another option is to pass the parameter in ipaw.nf on both cases and set a default value for splitchar in ipaw.nf.
Could you also write a short documentation in the Readme on when saavheader should be set and how. thanks