Error when running rnavar with --skip_intervallisttools option

[RaqManzano]

Description of the bug

I am getting an error when I test rnavar with the --skip_intervallisttools. It seems subworkflows like splincigars can only run with intervals, there is no adaptation without the intervals. Might be more dowstream but this is the first bottleneck when running with this option.`

Command used and terminal output

Command:

nextflow run main.nf -profile singularity,test --outdir results  --skip_intervallisttools

Error:

Invalid method invocation `call` with arguments: [[id:GM12878, single_end:false], /rds/project/rds-upenYb9rdtk/Work/rm889/rna/nextflow/rnavar/work/18/cc7a1c1283d17a4567f27f7359431d/GM12878.markdup.sorted.bam, /rds/project/rds-upenYb9rdtk/Work/rm889/rna/nextflow/rnavar/work/e4/644c309484417807c7a96eb251d50d/GM12878.markdup.sorted.bam.bai, [id:genome.bed], /rds/project/rds-upenYb9rdtk/Work/rm889/rna/nextflow/rnavar/work/24/cd83cb4b3b27fd39cd651a18537859/genome.bed.interval_list] (java.util.LinkedList) on _closure3 type

Relevant files

No response

System information

nf-core/rnavar v1.0.0

[KristinaGagalova]

Has this been addressed already? I have the same error