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Hi everyone ! I'm trying to run ONLY hifi reads bu...
# genomeassembler
s
Hi everyone ! I'm trying to run ONLY hifi reads but the pipeline is not getting initialised (Sample used is the test hifi reads provided in test config) command:- 
$ nextflow run nf-core/genomeassembler -profile hifi_flye,docker --input samplesheet.csv --outdir output_nf
samplesheet :- 
sample,hifireads
HiFi-Col-0_test,HiFi-Col-0_test_data.fastq.gz
n
Hi, can you run with 
-r dev
Not sure what is causing that error, but there have been some changes in the last months that should be released soonish, but I probably will not have time to sort out a new release before july
The error in the CLI is also not very helpful, I would need to see what 
.nextflow.log
for this actually contains to get an idea of what is going on..
s
Hi @Niklas Schandry please find log file attached same error after using -r dev .
nextflow.log
n
I think the path in the samplesheet needs to be an absolute path
s
I tried to change the samplesheet with absolute path find error log attached. 
sample,hifireads
HiFi-Col-0_test_data,/mnt/isilon/abiola/microbe-bioinfo/projects/Kleb-mcr8-CRE/HiFi_nf/HiFi-Col-0_test_data.fastq.gz
nextflow_abs.log
n
can you try with 
--use-ref false
?
s
nice catch we have to use two extra arguments to make this pipeline works with this kind of samplesheet. 
$nextflow run nf-core/genomeassembler -r dev -profile hifi_flye,docker --input samplesheet.csv --outdir output_nf --use_ref false --lift_annotations false
Do you think this should not happen while running pipeline without ref file it should handle it by its own?
may be some code refactor make it works let me know i can do some check on current code to improve its handling.
n
It is largely the case because I assumed that there would be more people running with some reference than without
✅ 1
but it would probably good to check if a reference is in the samplesheet if 
params.use_ref
is set to 
true
; same for the annotations
Part of the issue is the poor error message that falsely points to a container path value instead of a process input
Here is where that check should probably happen, please open a PR if you would like to contribute https://github.com/nf-core/genomeassembler/blob/dev/subworkflows/local/utils_nfcore_genomeassembler_pipeline/main.nf#L74
s
Make sense to me but error handling can be improve i will create a PR accordingly. thanks for the help !
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