Error executing process > 'NFCORE_NANOSEQ:NANOSEQ:RNA_FUSIONS_JAFFAL:UNTAR (null)'

[MustafaElshani]

I have been getting this error

Error executing process > 'NFCORE_NANOSEQ:NANOSEQ:RNA_FUSIONS_JAFFAL:UNTAR (null)'
 Caused by:
Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null)

 Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

Failed to invoke `workflow.onComplete` event handler 
 -- Check script '/root/.nextflow/assets/nf-core/nanoseq/./workflows/nanoseq.nf' at line: 524 or see '.nextflow.log' file for more details

This is the line I have run it with

nextflow run nf-core/nanoseq \ 

--input nanoseq_samplesheet.csv \ 

--outdir nf-core_NANOSEQ/ \ 

--protocol cDNA \ 

--skip_basecalling \ 

--skip_demultiplexing \ 

-profile docker \ 

--multiqc_title _LongRead_Nanopore_seq \ 

--save_align_intermeds  

Any help would be very much be appreciated

[duocang]

Hi.

do you fix this problem?

[amadaes]

Hi. I have also encountered this issue. Have you found any solutions yet? Thank you.

[christopher-hakkaart]

There was an issue with mapping. I've made a branch with the correct mapping and will merge it into dev soon. RNA_FUSIONS_JAFFAL is ram hungry so I'll investigate a way to reduce its requirements before merging.

[sunsetyerin]

Hi @christopher-hakkaart when will RNA_FUSIONS_JAFFAL be updated?
It seems like I cannot move forward from RNA_FUSIONS_JAFFAL error.

[christopher-hakkaart]

Have you tried the branch I mentioned above? Or is it to ram hungry for your setup?

[christopher-hakkaart]

I haven't tried full sized files but if you have access to some and could check it out for me that would be great

[christopher-hakkaart]

The branch is called fix_jaffal

[Jungal10]

untar the jaffar before hand and pointging to its folder worked for us

[christopher-hakkaart]

Thanks for the update - I've merged this fix into update_3_1 and will get the update out soon.