bacass does not run canu assebler when requested
SchwarzMarek opened this issue · 3 comments
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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|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
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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 : 5Relevant files
cano_not_executed.nextflow.log.zip
System information
running from interactive bash on Ubuntu 22.04.4 LTS
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_metadataalong withskip_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).
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. :)
Clossing this as it has been fixed in dev branch. Please, reopen it if necessary :)