Structural variation calling with singularity and EnsEMBL coordinates

[CDieterich]

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

2.5.1

Workflow Execution

Command line (Cluster)

Other workflow execution

No response

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-human-variation
--bam 'WT1_14_SNORD13_32_8_UL_gDNA_mapped.bam'
--ref '/biodb/genomes/homo_sapiens/GRCh38_102/GRCh38_102.fa'
--sample_name 'WT1_14_SNORD13_32_8'
--override_basecaller_cfg '[email protected]'
--snp
--mod
--cnv
--phased
--bam_min_coverage 10
--sv
-profile singularity

Workflow Execution - CLI Execution Profile

singularity

What happened?

The workflow above works fine if I do not use the --sv flag.
If I include it some tandem repeat finder files seems to use USCS coordinates as default (chrX).
However, I run on EnsEMBL coordinates (X only). Is there any way to correct for this via command line.

Relevant log output

Command error:
  Sniffles2 Error: A tandem repeat annotations file was provided, but no matching annotations were found for any contig in the sample input file. Please check if the contig naming scheme in the tandem repeat annotations matches with the one in the input sample file. (Fatal error, exiting.)

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

yes

Other demo data information

No response