bacass does not run canu assebler when requested

[SchwarzMarek]

Description of the bug

For some reson, canu is not running on ONT data (GenomeSize specified, reads provided with LongFastQ, R1, R2 and Fast5 are set to NA).

Command used and terminal output

nextflow run nf-core/bacass --input samples.tsv -profile docker --skip_kraken2 --outdir assembly --assembler canu --skip_kmerfinder --ncbi_assembly_metadata assembly_summary_refseq.txt --assembly_type long

 N E X T F L O W   ~  version 24.04.4

Launching `https://github.com/nf-core/bacass` [small_einstein] DSL2 - revision: c81202b770 [master]

WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`


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                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/bacass v2.3.1-gc81202b
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Core Nextflow options
  revision              : master
  runName               : small_einstein
  containerEngine       : docker
  launchDir             : /media/marek/4T/playground/bactass
  workDir               : /media/marek/4T/playground/bactass/work
  projectDir            : /home/marek/.nextflow/assets/nf-core/bacass
  userName              : marek
  profile               : docker
  configFiles           : 

Input/output options
  input                 : samples.tsv
  outdir                : assembly

Contamination Screening
  ncbi_assembly_metadata: assembly_summary_refseq.txt

Assembly parameters
  assembler             : canu
  assembly_type         : long
  canu_mode             : -nanopore

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

Skipping Options
  skip_kraken2          : true
  skip_kmerfinder       : true

!! Only displaying parameters that differ from the pipeline defaults !!
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If you use nf-core/bacass for your analysis please cite:

* 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
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executor >  local (5)
[e6/c28a85] NFCORE_BACASS:BACASS:NANOPLOT (BS518)           [100%] 2 of 2 ✔
[-        ] NFCORE_BACASS:BACASS:PYCOQC                     -
[ed/960f9a] NFCORE_BACASS:BACASS:PORECHOP_PORECHOP (LK4414) [100%] 2 of 2 ✔
[-        ] NFCORE_BACASS:BACASS:CANU                       -
[-        ] NFCORE_BACASS:BACASS:MEDAKA                     -
[-        ] NFCORE_BACASS:BACASS:QUAST                      -
[-        ] NFCORE_BACASS:BACASS:GUNZIP                     -
[-        ] NFCORE_BACASS:BACASS:PROKKA                     -
[f9/f50514] NFCORE_BACASS:BACASS:MULTIQC_CUSTOM (1)         [100%] 1 of 1 ✔
-[nf-core/bacass] Pipeline completed successfully-
Completed at: 11-Sep-2024 12:59:39
Duration    : 4m 5s
CPU hours   : 0.5
Succeeded   : 5

Relevant files

cano_not_executed.nextflow.log.zip

System information

running from interactive bash on Ubuntu 22.04.4 LTS

[Daniel-VM]

Hi @SchwarzMarek ,

Thanks for testing it out. in comming fix here #168 . It is going to be available in in revision dev. It may take a bit longer to include it in the upcoming 2.4.0 release.

Note: I noticed you added param.ncbi_assembly_metadata along with skip_kmerfinder. However, the NCBI file is only used when the KmerFinder step is activated. Otherwise, the pipeline will not use the NCBI assembly metadata. (specifically, the kmerfinder module uses the info in the NCBI txt file to download candidate reference genome).

[SchwarzMarek]

Thank you I'll test out the dev channel.

Ad Note ) That is residue from testing various options of the pipeline. Thanks for spotting it; I hope that it did not influence the pipeline performance. :)

[Daniel-VM]

Clossing this as it has been fixed in dev branch. Please, reopen it if necessary :)