ERROR ~ No such variable: coverage_report

[Surbhigrewal]

Description of the bug

I tried to run the treeval pipeline for the first time using the RAPID entry parameter to just create my curation files.
My directory structure is as below:
treeval
-assembly
--file.fa
-genomic_data
--arima_hic
---hic_reads.cram
---hic_reads.cram.crai
--pacbio
---fasta
----hifi_reads.fasta.gz
-sample.yaml

Command used and terminal output

nextflow run sanger-tol/treeval --input sample.yaml --output sample.pretext -entry RAPID -profile singularity

...
[-        ] RAP…VAL_RAPID:HIC_MAPPING:HIC_BAMTOBED_COOLER:SAMTOOLS_MARKDUP -
[-        ] RAP…REEVAL_RAPID:HIC_MAPPING:HIC_BAMTOBED_COOLER:BAMTOBED_SORT -
[-        ] RAP…PID:HIC_MAPPING:HIC_BAMTOBED_COOLER:GET_PAIRED_CONTACT_BED -
ERROR ~ No such variable: coverage_report

 -- Check script '/gpfs01/home/sbzsm11/.nextflow/assets/sanger-tol/treeval/./workflows/treeval_rapid.nf' at line: 161 or see '.nextflow.log' file for more details

Relevant files

nextflow.log
Vent10.yaml.zip

System information

HPC
nextflow version 24.10.1.5930
sanger-tol/treeval v1.1.1-g4c9f8cd

[DLBPointon]

Hi @Surbhigrewal

This is fixed in the upcoming v.1.2

We rushed a merge into dev too quickly and didn't instantiate a variable in all the entry points. We hope to get 1.2 out of the door before the end of the week.