ERROR ~ while scanning a simple key

[sitems]

Description of the bug

ERROR ~ while scanning a simple key
in 'reader', line 3, column 1:
0.4.8
^
could not find expected ':'
in 'reader', line 4, column 1:

^

Command used and terminal output

nextflow run nf-core/raredisease -r 2.1.0 -profile docker -with-dag dag.dot -work-dir workdir -resume -config $HOME/sav/genetics/code/nextflow-raredisease.config --genome GRCh38 --analysis_type wes --platform illumina --save_reference --input $HOME/sav/genetics/code/test_samplesheet_raredisease_uno.csv --outdir output --target_bed $HOME/biocache/raredisease/kits/S07604514_hg38/S07604514_Covered.bed --bait_padding 500 --intervals_wgs $HOME/biocache/raredisease/raredisease-master/assets/chr1-chr22chrXchrYchrM_grch38.interval_list --intervals_y $HOME/biocache/raredisease/raredisease-master/assets/chrY_grch38.interval_list --variant_catalog $HOME/biocache/raredisease/reference-files-master/rare-disease/disease_loci/ExpansionHunter-v5.0.0/variant_catalog_grch38.json --rmdup --run_mt_for_wes --skip_snv_annotation --skip_vep_filter --skip_sv_annotation --skip_mt_annotation --skip_germlinecnvcaller --skip_me_calling --skip_me_annotation --aligner bwa

Relevant files

No response

System information

Nextflow version: 24.04.4.5917
Hardware: Desktop
Executor:local
Container engine: Docker
OS: Ubuntu 22.04
Version of nf-core/raredisease: 2.1.0

[ramprasadn]

I wasn’t able to replicate the issue on my end. If you have a .nextflow.log file, could you please share it with us? That would be really helpful. Thank you!

[sitems]

.nextflow.log

[ramprasadn]

Hi @sitems! Looks like this might coming from peddy. I am still not able to replicate this issue on our end, but that's the only tool with the version string "0.4.8". Could you share the versions.yml file in your peddy work directory? And the versions.yaml file in the multiqc directory?

[sitems]

Hi, unfortunately, I removed all the files, and switched to --skip_peddy option, but I can confirm, that when it failed, I saw the peddy tool as the last in the terminal, so it is very likely that the error came from peddy. Good news is that I switched to 2.2.0 release today, and it works. So we can close this issue now.

[ramprasadn]

Glad to know that it worked with the latest version @sitems. I will close this issue.