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I’m trying to run this pipeline but I’m encounteri...
# bacass
m
I’m trying to run this pipeline but I’m encountering this weird error (see thread)
I ran:
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nextflow run nf-core/bacass -r 2.4.0 -c nextflow.config -profile singularity --input samplesheet.tsv  --skip_fastqc --skip_fastp --skip_kraken2 --skip_kmerfinder --outdir outputs/2024-11-26_15-KSA-samples_skip__fastp_fastqc_kraken2_kmerfinder
I got:
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Nextflow 24.10.1 is available - Please consider updating your version to it

 N E X T F L O W   ~  version 24.04.4

Launching `<https://github.com/nf-core/bacass>` [amazing_coulomb] DSL2 - revision: be9c064f57 [2.4.0]


------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/bacass 2.4.0
------------------------------------------------------
Input/output options
  input          : samplesheet.tsv
  outdir         : outputs/2024-11-26_15-KSA-samples_skip__fastp_fastqc_kraken2_kmerfinder

QC and Trim
  skip_fastqc    : true
  skip_fastp     : true

Assembly parameters
  canu_mode      : -nanopore

Annotation
  dfast_config   : /home/pampum/.nextflow/assets/nf-core/bacass/assets/test_config_dfast.py

Skipping Options
  skip_kraken2   : true
  skip_kmerfinder: true

Core Nextflow options
  revision       : 2.4.0
  runName        : amazing_coulomb
  containerEngine: singularity
  launchDir      : /ibex/user/pampum/2024-11-26_KSA-lib-ONT-assemblies
  workDir        : /ibex/user/pampum/2024-11-26_KSA-lib-ONT-assemblies/work
  projectDir     : /home/pampum/.nextflow/assets/nf-core/bacass
  userName       : pampum
  profile        : singularity
  configFiles    :

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------* The pipeline
  <https://doi.org/10.5281/zenodo.2669428>

* The nf-core framework
    <https://doi.org/10.1038/s41587-020-0439-x>

* Software dependencies
    <https://github.com/nf-core/bacass/blob/master/CITATIONS.md>

[-        ] NFCORE_BACASS:BACASS:CAT_FASTQ      -
[-        ] NFCORE_BACASS:BACASS:NANOPLOT       -
[-        ] NFCORE_BACASS:BACASS:CAT_FASTQ      -
[-        ] NFCORE_BACASS:BACASS:NANOPLOT       -
[-        ] NFCORE_BACASS:BACASS:PYCOQC         -
[-        ] NFCORE_BACASS:BACASS:UNICYCLER      -
[-        ] NFCORE_BACASS:BACASS:QUAST          -
[-        ] NFCORE_BACASS:BACASS:GUNZIP         -
[-        ] NFCORE_BACASS:BACASS:PROKKA         -
[-        ] NFCORE_BACASS:BACASS:MULTIQC_CUSTOM -
ERROR ~ Cannot invoke "java.nio.file.Path.getFileSystem()" because "path" is null

[-        ] NFCORE_BACASS:BACASS:CAT_FASTQ      -
[-        ] NFCORE_BACASS:BACASS:NANOPLOT       -
[-        ] NFCORE_BACASS:BACASS:PYCOQC         -
[-        ] NFCORE_BACASS:BACASS:UNICYCLER      -
[-        ] NFCORE_BACASS:BACASS:QUAST          -
[-        ] NFCORE_BACASS:BACASS:GUNZIP         -
[-        ] NFCORE_BACASS:BACASS:PROKKA         -
[-        ] NFCORE_BACASS:BACASS:MULTIQC_CUSTOM -
ERROR ~ Cannot invoke "java.nio.file.Path.getFileSystem()" because "path" is null

 -- Check script '/home/pampum/.nextflow/assets/nf-core/bacass/./workflows/../subworkflows/nf-core/utils_nfcore_pipeline/main.nf' at line: 97 or see '.nextflow.log' file for more details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>

 -- Check '.nextflow.log' file for details
Does anyone know what 
Cannot invoke "java.nio.file.Path.getFileSystem()" because "path" is null
means and why this is happening?
d
Is folder 
outputs
already existing?
m
Yes it is
I removed it and still got the same error
d
And the 
--outdir
doesnt contain any special characters or even a newline or such?
m
no this is all it is 
outputs/2024-11-26_15-KSA-samples_skip__fastp_fastqc_kraken2_kmerfinder
d
Hm ok, more: Did you run the pipeline successfully with 
-profile test
? If yes, could you attach the 
.nextflow.log
of the failed run?
m
Yeah I get the same error even with 
-profile singularity,test
Here’s the log
nextflow.log
d
The 
softwareVersionsToYAML
function is involved. It appears to occur when both 
--skip_fastqc
and 
--skip_fastp
are used together. When none of these software are used, it emmits a null value, which migth conflict with the 
softwareVersionsToYAML
function. https://github.com/nf-core/bacass/blob/be9c064f571ada41692f9e98f99474f16bf5c04b/subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf#L102
d
So the solution would be for now to not use 
--skip_fastqc
, i.e. allow fastqc to run if you indeed dont want to have fastp filtering your reads. To fix that bug in the longer run, 
.ifEmpty([])
should work I think.
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