Error when ONT only + dragonflye + nanopolish

[SchwarzMarek]

Description of the bug

Nanopolish doesn't run due to invalid input to MINIMAP2_POLISH step.

Command used and terminal output

N E X T F L O W   ~  version 24.04.4
Launching `https://github.com/nf-core/bacass` [modest_mccarthy] 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        : modest_mccarthy
containerEngine: docker
launchDir      : /mnt/c/Users/schwa/Downloads/jarmila_seq/assembly
workDir        : /mnt/c/Users/schwa/Downloads/jarmila_seq/assembly/work
projectDir     : /home/marek/.nextflow/assets/nf-core/bacass
userName       : marek
profile        : docker
configFiles    :
Input/output options
input
: bso.tsv
outdir         : dragon
Assembly parameters
assembler      : dragonflye
assembly_type  : long
canu_mode      : -nanopore
Assembly Polishing
polish_method  : nanopolish
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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[6f/554c23] NFCORE_BACASS:BACASS:NANOPLOT (80) | 1 of 1 ✔
[-        ] NFCORE_BACASS:BACASS:PYCOQC      -
[39/80855d] NFCORE_BACASS:BACASS:PORECHOP_PORECHOP (80) | 1 of 1 ✔
[5f/665232] NFCORE_BACASS:BACASS:DRAGONFLYE (80)        | 1 of 1 ✔
[-        ] NFCORE_BACASS:BACASS:MINIMAP2_POLISH        -
[-        ] NFCORE_BACASS:BACASS:SAMTOOLS_INDEX         -
[-        ] NFCORE_BACASS:BACASS:NANOPOLISH       -
[b0/5a4c5f] NFCORE_BACASS:BACASS:QUAST (report)         | 1 of 1 ✔
[-        ] NFCORE_BACASS:BACASS:GUNZIP       -
[09/d1667d] NFCORE_BACASS:BACASS:PROKKA (80) | 1 of 1 ✔
[-        ] NFCORE_BACASS:BACASS:MULTIQC_CUSTOM         -
-[nf-core/bacass] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_BACASS:BACASS:MINIMAP2_POLISH (1)'
Caused by:
Path value cannot be null
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '.nextflow.log' file for details

Relevant files

nextflow.log.zip

System information

Running on WSL2 with docker.

[Daniel-VM]

Clossing this as it has been fixed in #169. Please, reopen it if necessary :)