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nf-core / raredisease

Call and score variants from WGS/WES of rare disease patients.
https://nf-co.re/raredisease
MIT License
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ERROR ~ while scanning a simple key #603

Open sitems opened 3 weeks ago

sitems commented 3 weeks ago

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 commented 2 weeks ago

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 commented 2 weeks ago

.nextflow.log