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Hello, and thanks for this very useful pipeline! I...
# genomeassembler
i
Hello, and thanks for this very useful pipeline! I have previously run the pipeline to do an assembly which I have manually edited. Now I want to run the pipeline with 
--skip_assembly
, but it stops with an error before any jobs have been started:
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ERROR ~ Execution aborted due to an unexpected error
-- Check script '/home/user/.nextflow/assets/nf-core/genomeassembler/./workflows/../subworkflows/local/polishing/./medaka/polish_medaka/../../../liftoff/../../../modules/nf-core/liftoff/main.nf' at line: 6 or see '.nextflow.log' file for more details
Is there something wrong with my sample sheet or combination of parameters (see below)?
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# sample sheet
sample,ontreads,assembly,ref_fasta,ref_gff
duplex_q10_2000_c,/path/to/2025-11-07_duplex_2000_q10.fastq.gz,/path/to/2025-12-17_duplex_q10_2000_medaka.fa,/path/to/GCF_002775015.1_Cand_auris_B11221_V1_genomic.fasta,/path/to/GCF_002775015.1_Cand_auris_B11221_V1_genomic.gff

# command
nextflow run nf-core/genomeassembler -r 1.1.0 \
    -profile singularity \
    -config /path/to/nfcore.marvin.config \
    --input /path/to/genomeassembler/samplesheet.csv \
    --outdir /path/to/genomeassembler/ \
    --ont true \
    --use_ref true \
    --skip_assembly true \
    --jellyfish false \
    --merqury true \
    --quast true \
    --busco true \
    --busco_lineage saccharomycetes_odb10 \
    --lift_annotations true
n
I have to admit that the 
--skip-assembly
option was not tested very thoroughly
Do you have some more information on the error (from 
.nextflow.log
)?
I assume it is something about container being null?
i
There is this in the log file:
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jan.-27 11:17:39.413 [Actor Thread 10] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
 task: name=NFCORE_GENOMEASSEMBLER:GENOMEASSEMBLER:ASSEMBLE:QC:RUN_BUSCO:BUSCO (1); work-dir=null
 error [nextflow.exception.ProcessUnrecoverableException]: Path value cannot be null
jan.-27 11:17:39.415 [Actor Thread 12] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
 task: name=NFCORE_GENOMEASSEMBLER:GENOMEASSEMBLER:ASSEMBLE:RUN_LIFTOFF:LIFTOFF (1); work-dir=null
 error [nextflow.exception.ProcessUnrecoverableException]: Path value cannot be null
jan.-27 11:17:39.447 [Actor Thread 9] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
 task: name=NFCORE_GENOMEASSEMBLER:GENOMEASSEMBLER:ASSEMBLE:QC:RUN_BUSCO:BUSCO; work-dir=null
 error [java.lang.InterruptedException]: java.lang.InterruptedException
jan.-27 11:17:39.462 [Actor Thread 12] ERROR nextflow.processor.TaskProcessor - Execution aborted due to an unexpected error
java.lang.NullPointerException: Cannot get property 'containerEngine' on null object
n
ok
I will try to take a look..
So, this is obviously a bug, and it is tricky to work around. Essentially, the issue is that when 
--skip_assembly
is used, the reads that are used for mapping are not created correctly, since those come from the inputs for the assembler, and that step is skipped. Can you try the following, highly unintuitive combination:
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assembler = "hifiasm"
qc_reads = "ont"
hifi = true
ont = true
skip_assembly = true
👍 1
If that doesnt work, I think the only way to get this through qc would be to prepare the alignment and also use 
--skip_alignments
and provide an 
assembly_bam
via the samplesheet
i
Thanks for the suggestions! I will try tomorrow
n
ok, please let me know what (doesnt) work
i
I tried the first approach:
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nextflow run nf-core/genomeassembler -r 1.1.0 \
    -profile singularity \
    -config /path/to/nfcore.marvin.config \
    --input /path/to/genomeassembler/samplesheet.csv \
    --outdir /path/to/genomeassembler/ \
    --ont true \
    --hifi true \
    --assembler hifiasm \
    --qc_reads ONT \
    --use_ref true \
    --skip_assembly true \
    --jellyfish false \
    --merqury true \
    --quast true \
    --busco true \
    --busco_lineage saccharomycetes_odb10 \
    --lift_annotations true
But getting the same error as before. I will continue with your other suggestion
n
Hm, I think there is a second problem: https://github.com/nf-core/genomeassembler/blob/1.1.0/subworkflows/local/assemble/main.nf#L170 this else should be after the 
{
in the line above. If you feel comfortable editing this in your local clone maybe that would work.. I am sorry about this, but I currently have 0 capacity to fix this in that version, since I am working on the upcoming version with some fundamental differences. I will add a note about this bug
i
I will try that also, thank you!
n
Any success?
i
I was working on other projects, but was just getting back to this now…
👍 1
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