str:make_report fails when adding region to wf_str_repeats.bed file

[ilivyatan]

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v2.0.0-g52e3698

Workflow Execution

Command line (Local)

Other workflow execution

No response

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-human-variation -profile standard --snp --sv --cnv --str --sex male --bam --ref GCA_000001405.15.GRCh38_no_alt_analysis_set.fna --out-dir epi2me_out --basecaller_cfg '[email protected]' --sample-name ''

Workflow Execution - CLI Execution Profile

None

What happened?

pipeline failed after a couple hours on the str:make_report.
This came directly after I modified the wf_str_repeats.bed file in the data/ directory of the pipeline because I wanted to include on extra region.
When I reverted to the original file and reran with -resume, it ran smoothly.

Relevant log output

ERROR ~ Error executing process > 'str:make_report (1)'

Caused by:
  Process `str:make_report (1)` terminated with an error exit status (1)

Command executed:

  workflow-glue report_str             -o 51210_barcode08_sorted.wf-human-str-report.html             --params params.json             --sample_name 51210_barcode08_sorted             --version versions.txt             --vcf 51210_barcode08_sorted.wf_str.vcf.gz             --straglr 51210_barcode08_sorted.wf_str.straglr.tsv             --stranger 51210_barcode08_sorted_plot.tsv             --stranger_annotation 51210_barcode08_sorted_stranger.tsv             --str_content 51210_barcode08_sorted_str-content-all.csv             --read_stats 51210_barcode08_sorted.readstats.tsv.gz

Command exit status:
  1

Command output:
  (empty)

Command error:
  [13:50:56 - matplotlib.font_manager] generated new fontManager
  [13:50:57 - workflow_glue] Starting entrypoint.
  /home/prom/.nextflow/assets/epi2me-labs/wf-human-variation/bin/workflow_glue/report_str.py:578: DeprecationWarning: Explicitly passing 'active' parameter is deprecated and will be ignored.
    with tabs.add_tab("Mutation", True):
  /home/prom/.nextflow/assets/epi2me-labs/wf-human-variation/bin/workflow_glue/report_str.py:584: DeprecationWarning: Explicitly passing 'active' parameter is deprecated and will be ignored.
    with tabs.add_tab("Pre-mutation", False):
  /home/prom/.nextflow/assets/epi2me-labs/wf-human-variation/bin/workflow_glue/report_str.py:590: DeprecationWarning: Explicitly passing 'active' parameter is deprecated and will be ignored.
    with tabs.add_tab("Normal", False):
  Traceback (most recent call last):
    File "/home/prom/.nextflow/assets/epi2me-labs/wf-human-variation/bin/workflow-glue", line 7, in <module>
      cli()
    File "/home/prom/.nextflow/assets/epi2me-labs/wf-human-variation/bin/workflow_glue/__initexecutor >  local (2141)

Application activity log entry

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

yes

Other demo data information

[vlshesketh]

Hi @ilivyatan, thanks for your interest in the workflow. Unfortunately at this time you're not able to modify the wf_str_repeats.bed file in this way. However, we recognise that users would like to be able to specify their own repeats, and have a ticket internally to address it, but we don’t have a timeline to share just yet. Please stay tuned for future updates 🙂